How to build a pathogen detector: structural basis of NB-LRR function

Many plant disease resistance (R) proteins belong to the family of nucleotide-binding-leucine rich repeat (NB-LRR) proteins. NB-LRRs mediate recognition of pathogen-derived effector molecules and subsequently activate host defence. Their multi-domain structure allows these pathogen detectors to simultaneously act as sensor, switch and response factor. Structure-function analyses and the recent elucidation of the 3D structures of subdomains have provided new insight in how these different functions are combined and what the contribution is of the individual subdomains. Besides interdomain contacts, interactions with chaperones, the proteasome and effector baits are required to keep NB-LRRs in a signalling-competent, yet auto-inhibited state. In this review we explore operational models of NB-LRR functioning based on recent advances in understanding their structure.     

Receptor-like kinases and receptor-like proteins: keys to pathogen recognition and defense signaling in plant innate immunity

Plants have evolved multiple layers of defense against various pathogens in the environment. Receptor-like kinases/proteins (RLKs/RLPs) are on the front lines of the battle between plants and pathogens since they are present at the plasma membrane and perceive signature molecules from either the invading pathogen or damaged plant tissue. With a few notable exceptions, most RLKs/RLPs are positive regulators of plant innate immunity. In this review, we summarize recently discovered RLKs/RLPs that are involved in plant defense responses against various classes of pathogens.We also describe what is currently known about the mechanisms of RLK-mediated initiation of signaling via protein-protein interactions and phosphorylation.     

Plant NB-LRR immune receptors: from recognition to transcriptional reprogramming

Both plants and animals contain nucleotide-binding domain and leucine-rich repeat (NB-LRR)-type immune receptors that function during defense against pathogens. Unlike animal NB-LRRs that recognize general pathogen or microbe-associated molecular patterns (PAMPs or MAMPs), plant NB-LRR immune receptors have evolved the ability to specifically recognize a wide range of effector proteins from different pathogens. Recent research has revealed that plant NB-LRRs are incredibly adaptive in their ways of pathogen recognition and defense initiation. This review focuses on the remarkable variety of functions, recognition mechanisms, subcellular localizations, and host factors associated with plant NB-LRR immune receptors.     

Nep1-like proteins as a target for plant pathogen control

The lack of efficient methods to control the major diseases of crops most important to agriculture leads to huge economic losses and seriously threatens global food security. Many of the most important microbial plant pathogens, including bacteria, fungi, and oomycetes, secrete necrosis- and ethylene-inducing peptide 1 (Nep1)-like proteins (NLPs), which critically contribute to the virulence and spread of the disease. NLPs are cytotoxic to eudicot plants, as they disturb the plant plasma membrane by binding to specific plant membrane sphingolipid receptors. Their pivotal role in plant infection and broad taxonomic distribution makes NLPs a promising target for the development of novel phytopharmaceutical compounds. To identify compounds that bind to NLPs from the oomycetes Pythium aphanidermatum and Phytophthora parasitica, a library of 587 small molecules, most of which are commercially unavailable, was screened by surface plasmon resonance. Importantly, compounds that exhibited the highest affinity to NLPs were also found to inhibit NLP-mediated necrosis in tobacco leaves and Phytophthora infestans growth on potato leaves. Saturation transfer difference-nuclear magnetic resonance and molecular modelling of the most promising compound, anthranilic acid derivative, confirmed stable binding to the NLP protein, which resulted in decreased necrotic activity and reduced ion leakage from tobacco leaves. We, therefore, confirmed that NLPs are an appealing target for the development of novel phytopharmaceutical agents and strategies, which aim to directly interfere with the function of these major microbial virulence factors. The compounds identified in this study represent lead structures for further optimization and antimicrobial product development.     

Perturbation of host ubiquitin systems by plant pathogen/pest effector proteins

Microbial pathogens and pests of animals and plants secrete effector proteins into host cells, altering cellular physiology to the benefit of the invading parasite. Research in the past decade has delivered significant new insights into the molecular mechanisms of how these effector proteins function, with a particular focus on modulation of host immunity‐related pathways. One host system that has emerged as a common target of effectors is the ubiquitination system in which substrate proteins are post‐translationally modified by covalent conjugation with the small protein ubiquitin. This modification, typically via isopeptide bond formation through a lysine side chain of ubiquitin, can result in target degradation, relocalization, altered activity or affect protein–protein interactions. In this review, I focus primarily on how effector proteins from bacterial and filamentous pathogens of plants and pests perturb host ubiquitination pathways that ultimately include the 26S proteasome. The activities of these effectors, in how they affect ubiquitin pathways in plants, reveal how pathogens have evolved to identify and exploit weaknesses in this system that deliver increased pathogen fitness.     

In the trenches: lessons for scientists from California's Proposition 71 campaign

I describe a number of valuable lessons I learned from participating in California's Proposition 71 effort about the role that scientists and rigorous scientific advice can play in a public political process. I describe how scientists can provide valuable information and advice and how they can also gain a great deal from the experience that is valuable to a practicing research scientist. Finally, I argue that in the future, building similar broad coalitions to support biomedical and other areas of scientific research will be essential to protect publicly funded science. Thus, a key lesson from the Proposition 71 experience is that engagement of scientists with diverse nonscientific groups can make a big difference and that scientists must actively engage with the public in the future if we are to contribute robustly to the medical and economic health of our communities.     

Type III effector proteins from the plant pathogen Xanthomonas and their role in the interaction with the host plant

Pathogenicity of Xanthomonas campestris pathovar (pv.) vesicatoria and most other Gram-negative bacterial plant pathogens largely depends on a type III secretion (TTS) system which is encoded by hypersensitive response and pathogenicity (hrp) genes. These genes are induced in the plant and are essential for the bacterium to be virulent in susceptible hosts and for the induction of the hypersensitive response (HR) in resistant host and non-host plants. The TTS machinery secretes proteins into the extracellular milieu and effector proteins into the plant cell cytosol. In the plant, the effectors presumably interfere with cellular processes to the benefit of the pathogen or have an avirulence activity that betrays the bacterium to the plant surveillance system. Type III effectors were identified by their avirulence activity, co-regulation with the TTS system and homology to known effectors. A number of effector proteins are members of families, e.g., the AvrBs3 family in Xanthomonas. AvrBs3 localizes to the nucleus of the plant cell where it modulates plant gene expression. Another family that is also present in Xanthomonas is the YopJ/AvrRxv family. The latter proteins appear to act as SUMO cysteine proteases in the host. Here, we will present an overview about the regulation of the TTS system and its substrates and discuss the function of the AvrRxv and AvrBs3 family members in more detail.     

Role of plant lipid transfer proteins in plant cell physiology-a concise review

Plant lipid transfer proteins (LTP) are cationic peptides, subdivided into two families, which present molecular masses of around 7 and 10 kDa. The peptides were, thus, denominated due to their ability to reversibly bind and transport hydrophobic molecules in vitro. Both subfamilies possess conserved patterns of eight cysteine residues and the three-dimensional structure reveals an internal hydrophobic cavity that comprises the lipid binding site. Based on the growing knowledge regarding structure, gene expression and regulation and in vitro activity, LTPs are likely to play a role in key processes of plant physiology. Although the roles of plant LTPs have not yet been fully determined. This review aims to present comprehensive information of recent topics, cover new additional data, and present new perspectives on these families of peptides.     

Identification of 18 genes encoding necrosis-inducing proteins from the plant pathogen Phytophthora capsici (Pythiaceae: Oomycetes)

Phytophthora capsici is an aggressive plant pathogen that affects solanaceous and cucurbitaceous hosts. Necrosis-inducing Phytophthora proteins (NPPs) are a group of secreted toxins found particularly in oomycetes. Several NPPs from Phytophthora species trigger plant cell death and activate host defense gene expression. We isolated 18 P. capsici NPP genes, of which 12 were active during hypha growth from a Phytophthora stain isolated from pepper (Capsicum annuum) plants in China. The 18 predicted proteins had a sequence homology of 46.26%. The 18 Pcnpp sequences had a conserved GHRHDWE motif and fell into two groups. Eleven sequences in group 1 had two conserved cysteine residues, whereas the other seven sequences in group 2 lacked these two cysteine residues. A phylogenetic tree was constructed on the basis of the alignment of the predicted protein sequences of 52 selected NPP genes from oomycetes, fungi and bacteria from Genbank. The tree did not rigorously follow the taxonomic classification of the species; all the NPPs from oomycetes formed their own clusters, while fungal sequences were grouped into two separate clades, indicating that based on NPPs, we can separate oomycetes from fungi and bacteria, and that expansion of the NPP family was a feature of Phytophthora evolution.     

Biotechnological potential of engineering pathogen effector proteins for use in plant disease management

A key component in the management of many diseases of crops is the use of plant disease resistance genes. However, the discovery and then sequence identification of these plant genes is challenging, whereas the characterization of the molecules that they recognize, the effector/avirulence products in pathogens, is often considerably more straight forward. Effectors are small proteins secreted by pathogens that can play major roles in modulating a plant's defense against attack. Effectors can be used to guide breeding of resistance genes, to trigger defense responses, and are part of integrated disease management strategies for crop protection. This review covers the role of effector-driven biotechnology in controlling plant diseases caused by fungi or oomycetes. Given that multi-billion dollar agriculture crops are based in some cases on plants recognizing just a handful of such effector proteins, there is considerable scope to use more fully effector proteins as a biotechnology resource in agriculture.     

Enterobacter agglomerans: the clinically important plant pathogen.

During a 5-month period Enterobacter agglomerans, now described as a member of the phytopathogenic genus Erwinia, was isolated from 13 patients in a general hospital; in 1 patient it was isolated from two sites. In six instances the organism was the sole pathogen isolated, in two instances it may have contributed to infection and in the remaining instances it was probably a transient saprophyte. The strains showed some variation in biochemical reactions but were similar in colonial morphology and were consistently sensitive to several antibiotics. Although this organism is prevalent in the general environment and usually relatively benign, it does have a potential for nosocomial infection.     

Pantoea ananatis: an unconventional plant pathogen

Pantoea ananatis causes disease symptoms in a wide range of economically important agricultural crops and forest tree species worldwide. It is regarded as an emerging pathogen based on the increasing number of reports of diseases occurring on previously unrecorded hosts in different parts of the world. Its unconventional nature lies in the fact that, unlike the majority of plant pathogenic microbes, P. ananatis is capable of infecting humans and occurs in diverse ecological niches, such as part of a bacterial community contaminating aviation jet fuel tanks and contributing to growth promotion in potato and pepper.
Taxonomy: Bacteria; Gammaproteobacteria ; family Enterobacteriaceae ; genus Pantoea.
Microbiological properties: Gram-negative; facultatively anaerobic; most strains are motile and produce a yellow pigment in culture; indole positive.
Biology: Pantoea ananatis is a common epiphyte; it also occurs endophytically in hosts where it has been reported to cause disease symptoms and in hosts where no such symptoms have been described. Some strains are ice-nucleating, a feature which has been used as a biological control mechanism against some insect pests of agricultural crops and by the food industry.
Disease symptoms: Pantoea ananatis infects both monocotyledonous and dicotyledonous plants. The symptoms are diverse depending on the host infected, and include leaf blotches and spots, die-back, and stalk, fruit and bulb rot.
Biological control agent: Pantoea ananatis has both antifungal and antibacterial properties. These characteristics have the potential of being exploited by biological control specialists.     

In the autophagy trenches: The early research career of Russell L. Deter

Christian de Duve is considered to be one of the founding fathers of autophagy. After all, he coined the term, and he played an instrumental role in the discovery of the lysosome, for which he received the Nobel Prize. There is no question that de Duve is a stellar scientist, but who was the person in the trenches, doing the actual laboratory work in the lab that led to the initial papers on autophagy? Dr. Russell L. Deter wrote the first papers from the de Duve lab that deal with this topic. To get some insight into the origins of this field, I interviewed Dr. Deter, as detailed in this perspective.     

Proteomics of a plant pathogen: Agrobacterium tumefaciens

Agrobacterium tumefaciens is an important plant pathogen which belongs to the α-proteobacteria. In addition, it has served as the main tool for plant molecular genetics. Here we focus on three major aspects: (i) proteomic mapping, (ii) the use of proteomics for the understanding of the response of A. tumefaciens to changes in environmental conditions and (iii) the analysis of the changes in genome expression following interaction with the host. These studies convey a global outlook on the functional genomics of A. tumefaciens and help to understand the physiology of this important organism.     

From pathogen genomes to host plant processes: the power of plant parasitic oomycetes

Recent pathogenomic research on plant parasitic oomycete effector function and plant host responses has resulted in major conceptual advances in plant pathology, which has been possible thanks to the availability of genome sequences.