Advances and perspectives in discovery and functional analysis of small secreted proteins in plants

AbstractSmall secreted proteins (SSPs) are less than 250 amino acids in length and are actively transported out of cells through conventional protein secretion pathways or unconventional protein secretion pathways. In plants, SSPs have been found to play important roles in various processes, including plant growth and development, plant response to abiotic and biotic stresses, and beneficial plant–microbe interactions. Over the past 10 years, substantial progress has been made in the identification and functional characterization of SSPs in several plant species relevant to agriculture, bioenergy, and horticulture. Yet, there are potentially a lot of SSPs that have not been discovered in plant genomes, which is largely due to limitations of existing computational algorithms. Recent advances in genomics, transcriptomics, and proteomics research, as well as the development of new computational algorithms based on machine learning, provide unprecedented capabilities for genome-wide discovery of novel SSPs in plants. In this review, we summarize known SSPs and their functions in various plant species. Then we provide an update on the computational and experimental approaches that can be used to discover new SSPs. Finally, we discuss strategies for elucidating the biological functions of SSPs in plants.

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The Road Less Traveled? Unconventional Protein Secretion at Parasite–Host Interfaces

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.662711 ◽

2021 ◽

Vol 9 ◽

Author(s):

Erina A. Balmer ◽

Carmen Faso

Keyword(s):

Protein Secretion ◽

Cell Biology ◽

Mammalian Cells ◽

Cell Model ◽

Signal Sequence ◽

Model Organism ◽

Secreted Proteins ◽

Current Status ◽

Secretory Proteins ◽

Secretion Pathways

Protein secretion in eukaryotic cells is a well-studied process, which has been known for decades and is dealt with by any standard cell biology textbook. However, over the past 20 years, several studies led to the realization that protein secretion as a process might not be as uniform among different cargos as once thought. While in classic canonical secretion proteins carry a signal sequence, the secretory or surface proteome of several organisms demonstrated a lack of such signals in several secreted proteins. Other proteins were found to indeed carry a leader sequence, but simply circumvent the Golgi apparatus, which in canonical secretion is generally responsible for the modification and sorting of secretory proteins after their passage through the endoplasmic reticulum (ER). These alternative mechanisms of protein translocation to, or across, the plasma membrane were collectively termed “unconventional protein secretion” (UPS). To date, many research groups have studied UPS in their respective model organism of choice, with surprising reports on the proportion of unconventionally secreted proteins and their crucial roles for the cell and survival of the organism. Involved in processes such as immune responses and cell proliferation, and including far more different cargo proteins in different organisms than anyone had expected, unconventional secretion does not seem so unconventional after all. Alongside mammalian cells, much work on this topic has been done on protist parasites, including genera Leishmania, Trypanosoma, Plasmodium, Trichomonas, Giardia, and Entamoeba. Studies on protein secretion have mainly focused on parasite-derived virulence factors as a main source of pathogenicity for hosts. Given their need to secrete a variety of substrates, which may not be compatible with canonical secretion pathways, the study of mechanisms for alternative secretion pathways is particularly interesting in protist parasites. In this review, we provide an overview on the current status of knowledge on UPS in parasitic protists preceded by a brief overview of UPS in the mammalian cell model with a focus on IL-1β and FGF-2 as paradigmatic UPS substrates.

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The Emerging Mechanisms of Wnt Secretion and Signaling in Development

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.714746 ◽

2021 ◽

Vol 9 ◽

Author(s):

Shefali Mehta ◽

Swapnil Hingole ◽

Varun Chaudhary

Keyword(s):

Signaling Pathways ◽

Protein Secretion ◽

Extracellular Space ◽

Tissue Homeostasis ◽

Secreted Proteins ◽

Complex Interplay ◽

The Past ◽

Signaling Mechanisms ◽

Protein Gradients ◽

Multiple Signaling

Wnts are highly-conserved lipid-modified secreted proteins that activate multiple signaling pathways. These pathways regulate crucial processes during various stages of development and maintain tissue homeostasis in adults. One of the most fascinating aspects of Wnt protein is that despite being hydrophobic, they are known to travel several cell distances in the extracellular space. Research on Wnts in the past four decades has identified several factors and uncovered mechanisms regulating their expression, secretion, and mode of extracellular travel. More recently, analyses on the importance of Wnt protein gradients in the growth and patterning of developing tissues have recognized the complex interplay of signaling mechanisms that help in maintaining tissue homeostasis. This review aims to present an overview of the evidence for the various modes of Wnt protein secretion and signaling and discuss mechanisms providing precision and robustness to the developing tissues.

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In Silico Prediction and Functional Characterization of Genes Related to Abiotic and Biotic Stresses in Chickpea (Cicer arietinum)

Current Research in Bioinformatics ◽

10.3844/ajbsp.2018.1.35 ◽

2018 ◽

Vol 7 (1) ◽

pp. 1-35

Author(s):

Sukhdeep Kaur ◽

Satendra Singh ◽

Gitanjali Tandon ◽

Sarika Jaiswal ◽

Mir Asif Iquebal ◽

...

Keyword(s):

Cicer Arietinum ◽

In Silico ◽

Functional Characterization ◽

In Silico Prediction ◽

Abiotic And Biotic Stresses ◽

Biotic Stresses

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Evaluation of virus-induced gene silencing methods for forage legumes including alfalfa, sainfoin, and fenugreek

Canadian Journal of Plant Science ◽

10.1139/cjps-2018-0329 ◽

2019 ◽

Vol 99 (6) ◽

pp. 917-926 ◽

Cited By ~ 2

Author(s):

Champa Wijekoon ◽

Stacy D. Singer ◽

Randall J. Weselake ◽

Udaya Subedi ◽

Surya N. Acharya

Keyword(s):

Gene Silencing ◽

Plant Species ◽

Reverse Genetics ◽

Functional Characterization ◽

Homologous Gene ◽

Virus Induced Gene Silencing ◽

Forage Legumes ◽

Crop Species ◽

Barrel Medic ◽

Trigonella Foenum Graecum L

Virus-induced gene silencing (VIGS) is a rapid reverse genetics tool that has been developed in a wide variety of plant species for assessing gene functions. However, while VIGS has been utilized successfully in the diploid model leguminous species Medicago truncatula (Gaertn.) (barrel medic), such a platform has yet to be established in forage legume crop species. Therefore, we evaluated the effectiveness of this method in forage legumes using a previously developed PEBV (pea early browning virus) system whereby a fragment of the pea (Pisum sativum L.) PHYTOENE DESATURASE (PDS) gene was transferred into a range of alfalfa (Medicago sativa L.), sainfoin (Onobrychis viciifolia Scop.), and fenugreek (Trigonella foenum-graecum L.) cultivars using leaf infiltration and apical meristem injection. Barrel medic was used as a positive control. Gene silencing was observed after 10–15 d through the presence of a leaf bleaching phenotype, and was confirmed using quantitative real-time RT-PCR. Silencing of PDS was achieved in a selection of cultivars in all species assessed, with the highest silencing efficiency apparent in fenugreek. The introduction of a highly homologous gene fragment from a heterologous plant species to target endogenous genes for transient VIGS-based silencing in a range of species of interest represents a potentially useful strategy for the rapid functional characterization of candidate genes in forages.

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RAB6 and microtubules restrict protein secretion to focal adhesions

The Journal of Cell Biology ◽

10.1083/jcb.201805002 ◽

2019 ◽

Vol 218 (7) ◽

pp. 2215-2231 ◽

Cited By ~ 32

Author(s):

Lou Fourriere ◽

Amal Kasri ◽

Nelly Gareil ◽

Sabine Bardin ◽

Hugo Bousquet ◽

...

Keyword(s):

Endoplasmic Reticulum ◽

Plasma Membrane ◽

Cell Surface ◽

Protein Secretion ◽

Golgi Complex ◽

Essential Role ◽

Focal Adhesions ◽

Secreted Proteins ◽

Cell Compartments ◽

Secretion Assay

To ensure their homeostasis and sustain differentiated functions, cells continuously transport diverse cargos to various cell compartments and in particular to the cell surface. Secreted proteins are transported along intracellular routes from the endoplasmic reticulum through the Golgi complex before reaching the plasma membrane along microtubule tracks. Using a synchronized secretion assay, we report here that exocytosis does not occur randomly at the cell surface but on localized hotspots juxtaposed to focal adhesions. Although microtubules are involved, the RAB6-dependent machinery plays an essential role. We observed that, irrespective of the transported cargos, most post-Golgi carriers are positive for RAB6 and that its inactivation leads to a broad reduction of protein secretion. RAB6 may thus be a general regulator of post-Golgi secretion.

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The influence of warming and biotic interactions on the potential for range expansion of native and nonnative species

AoB Plants ◽

10.1093/aobpla/plaa040 ◽

2020 ◽

Vol 12 (5) ◽

Author(s):

Betsy von Holle ◽

Sören E Weber ◽

David M Nickerson

Keyword(s):

Plant Species ◽

Range Expansion ◽

Species Interactions ◽

Native Species ◽

Invasive Plant ◽

Soil Microbes ◽

Enemy Release ◽

Native Plant ◽

Soil Pathogens ◽

Microbe Interactions

Abstract Plant species ranges are expected to shift in response to climate change, however, it is unclear how species interactions will affect range shifts. Because of the potential for enemy release of invasive nonnative plant species from species-specific soil pathogens, invasive plants may be able to shift ranges more readily than native plant species. Additionally, changing climatic conditions may alter soil microbial functioning, affecting plant–microbe interactions. We evaluated the effects of site, plant–soil microbe interactions, altered climate, and their interactions on the growth and germination of three congeneric shrub species, two native to southern and central Florida (Eugenia foetida and E. axillaris), and one nonnative invasive from south America (E. uniflora). We measured germination and biomass for these plant species in growth chambers grown under live and sterile soils from two sites within their current range, and one site in their expected range, simulating current (2010) and predicted future (2050) spring growing season temperatures in the new range. Soil microbes (microscopic bacteria, fungi, viruses and other organisms) had a net negative effect on the invasive plant, E. uniflora, across all sites and temperature treatments. This negative response to soil microbes suggests that E. uniflora’s invasive success and potential for range expansion are due to other contributing factors, e.g. higher germination and growth relative to native Eugenia. The effect of soil microbes on the native species depended on the geographic provenance of the microbes, and this may influence range expansion of these native species.

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