Over the past decade, the Nomenclature Committee on Cell Death (NCCD) has formulated guidelines for the definition and interpretation of cell death from morphological, biochemical, and functional perspectives. Since the field continues to expand and novel mechanisms that orchestrate multiple cell death pathways are unveiled, we propose an updated classification of cell death subroutines focusing on mechanistic and essential (as opposed to correlative and dispensable) aspects of the process. As we provide molecularly oriented definitions of terms including intrinsic apoptosis, extrinsic apoptosis, mitochondrial permeability transition (MPT)-driven necrosis, necroptosis, ferroptosis, pyroptosis, parthanatos, entotic cell death, NETotic cell death, lysosome-dependent cell death, autophagy-dependent cell death, immunogenic cell death, cellular senescence, and mitotic catastrophe, we discuss the utility of neologisms that refer to highly specialized instances of these processes. The mission of the NCCD is to provide a widely accepted nomenclature on cell death in support of the continued development of the field.

https://biblio.ugent.be/publication/8555786/file/8555788.pdf

Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018.

Microbe-associated molecular patterns (MAMPs) are molecular signatures typical of whole classes of microbes, and their recognition plays a key role in innate immunity. Endogenous elicitors are similarly recognized as damage-associated molecular patterns (DAMPs). This review focuses on the diversity of MAMPs/DAMPs and on progress to identify the corresponding pattern recognition receptors (PRRs) in plants. The two best-characterized MAMP/PRR pairs, flagellin/FLS2 and EF-Tu/EFR, are discussed in detail and put into a phylogenetic perspective. Both FLS2 and EFR are leucine-rich repeat receptor kinases (LRR-RKs). Upon treatment with flagellin, FLS2 forms a heteromeric complex with BAK1, an LRR-RK that also acts as coreceptor for the brassinolide receptor BRI1. The importance of MAMP/PRR signaling for plant immunity is highlighted by the finding that plant pathogens use effectors to inhibit PRR complexes or downstream signaling events. Current evidence indicates that MAMPs, DAMPs, and effectors are all perceived as danger signals and induce a stereotypic defense response.

A Renaissance of Elicitors: Perception of Microbe-Associated Molecular Patterns and Danger Signals by Pattern-Recognition Receptors

In 2009, the Nomenclature Committee on Cell Death (NCCD) proposed a set of recommendations for the definition of distinct cell death morphologies and for the appropriate use of cell death-related terminology, including 'apoptosis', 'necrosis' and 'mitotic catastrophe'. In view of the substantial progress in the biochemical and genetic exploration of cell death, time has come to switch from morphological to molecular definitions of cell death modalities. Here we propose a functional classification of cell death subroutines that applies to both in vitro and in vivo settings and includes extrinsic apoptosis, caspase-dependent or -independent intrinsic apoptosis, regulated necrosis, autophagic cell death and mitotic catastrophe. Moreover, we discuss the utility of expressions indicating additional cell death modalities. On the basis of the new, revised NCCD classification, cell death subroutines are defined by a series of precise, measurable biochemical features.

/pdf/molecular-definitions-of-cell-death-subroutines-q5g428rlyi.pdf

Molecular definitions of cell death subroutines: recommendations of the Nomenclature Committee on Cell Death 2012

Autophagy is a mechanism by which cellular material is delivered to lysosomes for degradation, leading to the basal turnover of cell components and providing energy and macromolecular precursors. Autophagy has opposing, context-dependent roles in cancer, and interventions to both stimulate and inhibit autophagy have been proposed as cancer therapies. This has led to the therapeutic targeting of autophagy in cancer to be sometimes viewed as controversial. In this Review, we suggest a way forwards for the effective targeting of autophagy by understanding the context-dependent roles of autophagy and by capitalizing on modern approaches to clinical trial design.

/pdf/targeting-autophagy-in-cancer-2pjcn0h04a.pdf

Targeting autophagy in cancer

Much of plant physiology, growth, and development is controlled by the selective removal of short-lived regulatory proteins. One important proteolytic pathway involves the small protein ubiquitin (Ub) and the 26S proteasome, a 2-MDa protease complex. In this pathway, Ub is attached to proteins destined for degradation; the resulting Ub-protein conjugates are then recognized and catabolized by the 26S proteasome. This review describes our current understanding of the pathway in plants at the biochemical, genomic, and genetic levels, using Arabidopsis thaliana as the model. Collectively, these analyses show that the Ub/26S proteasome pathway is one of the most elaborate regulatory mechanisms in plants. The genome of Arabidopsis encodes more than 1400 (or >5% of the proteome) pathway components that can be connected to almost all aspects of its biology. Most pathway components participate in the Ub-ligation reactions that choose with exquisite specificity which proteins should be ubiquitinated. What remains to be determined is the identity of the targets, which may number in the thousands in plants.

/pdf/the-ubiquitin-26s-proteasome-proteolytic-pathway-3szv2gdxjk.pdf

The ubiquitin 26S proteasome proteolytic pathway

The S-locus of Brassica contains the genetic information that encodes for self-incompatibility. In its first aspect, it is directed to an isolated gene, the SRK-910 gene, that segregates with the self-incompatibility phenotype. In its second aspect, the present invention is directed to an isolated cDNA that corresponds to the isolated gene and that has 2749 nucleotides. The isolated cDNA of the present invention encodes for a protein, i.e., the S-locus receptor kinase-910 protein ("the SRK-910 protein") which is also a part of the present invention. The SRK-910 protein, has 858 amino acids and is encoded for by the first 2575 nucleotides of the isolated cDNA of the present invention. The present invention is also directed to an oligonucleotide probe that is capable of distinguishing the SRK-910 gene from partially homologous genes at the S-locus that encode for the S-locus glycoproteins. The present invention is also directed to a transfer vector comprising the cDNA for the SLG-910 allele in combination with the cDNA of claim 1. Finally, the present invention is also directed to a method for conferring the self-incompatible phenotype on a self-compatible plant comprising transferring the disclosed transfer vector into a plant that is capable of assimilating the transfer vector and expressing self-incompatibility.

S-locus receptor kinase gene in a self-incompatible brassica napus line

A cytotoxic effect associated with 9-(1,3-dihydroxy-2-propoxymethyl)-guanine is observed during the selection for drug resistant human cells containing a single herpesvirus thymidine kinase gene.

Different versions of the same gene can be either dominant or recessive. A small non-coding RNA mediates such differences in dominance as part of a system that prevents inbreeding in plants.

Gene expression: How plants avoid incest.

The initial events of pollen–pistil interactions are fundamentally important in flowering plants because they influence successful fertilization. These early events include the recognition of pollen grains through signaling events in the pistil that will lead to the acceptance of a compatible pollen grain or the rejection of an incompatible pollen grain. There has been much research into this field in the Brassicaceae, as this family includes many agriculturally important crops such as canola, radish, turnip, and cabbage. However, this review focuses on what is known about the early pollen–pistil interactions in the experimentally tractable Arabidopsis genus, including Arabidopsis thaliana (a self-compatible species) and Arabidopsis lyrata (a self-incompatible species). Compatible pollinations are driven by the ability of the pistil to provide the resources for an acceptable pollen grain to hydrate, germinate, and fertilize the ovule. Self-incompatible species have a receptor–ligand signaling pathway that rejects self-pollen grains, preventing inbreeding and encouraging genetic diversity within the species. There is some overlap between these two pathways, and current research is looking for unknown elements and downstream events following the initial recognition of a pollen grain in Arabidopsis.

/pdf/signaling-events-in-pollen-acceptance-or-rejection-in-the-2qk114exmt.pdf

Daphne R. Goring

Papers

S-locus receptor kinase gene in a self-incompatible brassica napus line

A cytotoxic effect associated with 9-(1,3-dihydroxy-2-propoxymethyl)-guanine is observed during the selection for drug resistant human cells containing a single herpesvirus thymidine kinase gene.

Gene expression: How plants avoid incest.

Signaling Events in Pollen Acceptance or Rejection in the Arabidopsis Species

Characterization of a novel Brassica napus kinase, BNK1