Towards genomic and proteomic studies of protein phosphorylation in plant-pathogen interactions

Ustilaginoidea virens secretes a family of phosphatases that stabilize the negative immune regulator OsMPK6 and suppress plant immunity

Rice false smut caused by Ustilaginoidea virens is emerging as a devastating disease of rice (Oryza sativa) worldwide; however, the molecular mechanisms underlying U. virens virulence and pathogenicity remain largely unknown. Here we demonstrate that the small cysteine-rich secreted protein SCRE6 in U. virens is translocated into host cells during infection as a virulence factor. Knockout of SCRE6 leads to attenuated U. virens virulence to rice. SCRE6 and its homologs in U. virens function as a novel family of mitogen-activated protein kinase phosphatases harboring no canonical phosphatase motif. SCRE6 interacts with and dephosphorylates the negative immune regulator OsMPK6 in rice, thus enhancing its stability and suppressing plant immunity. Ectopic expression of SCRE6 in transgenic rice promotes pathogen infection by suppressing the host immune responses. Our results reveal a previously unidentified fungal infection strategy in which the pathogen deploys a family of tyrosine phosphatases to stabilize a negative immune regulator in the host plant to facilitate its infection.

Identification of Candidate Genes for a Major Quantitative Disease Resistance Locus From Soybean PI 427105B for Resistance to Phytophthora sojae

Phytophthora root and stem rot is a yield-limiting soybean disease caused by the soil-borne oomycete Phytophthora sojae. Although multiple quantitative disease resistance loci (QDRL) have been identified, most explain <10% of the phenotypic variation (PV). The major QDRL explaining up to 45% of the PV were previously identified on chromosome 18 and represent a valuable source of resistance for soybean breeding programs. Resistance alleles from plant introductions 427105B and 427106 significantly increase yield in disease-prone fields and result in no significant yield difference in fields with less to no disease pressure. In this study, high-resolution mapping reduced the QDRL interval to 3.1 cm, and RNA-seq analysis of near-isogenic lines (NILs) varying at QDRL-18 pinpointed a single gene of interest which was downregulated in inoculated NILs carrying the resistant allele compared to inoculated NILs with the susceptible allele. This gene of interest putatively encodes a serine-threonine kinase (STK) related to the AtCR4 family and may be acting as a susceptibility factor, based on the specific increase of jasmonic acid concentration in inoculated NILs. This work facilitates further functional analyses and marker-assisted breeding efforts by prioritizing candidate genes and narrowing the targeted region for introgression.

Phosphorylation of the Pseudomonas Effector AvrPtoB by Arabidopsis SnRK2.8 Is Required for Bacterial Virulence

A critical component controlling bacterial virulence is the delivery of pathogen effectors into plant cells during infection. Effectors alter host metabolism and immunity for the benefit of pathogens. Multiple effectors are phosphorylated by host kinases, and this posttranslational modification is important for their activity. We sought to identify host kinases involved in effector phosphorylation. Multiple phosphorylated effector residues matched the proposed consensus motif for the plant calcium-dependent protein kinase (CDPK) and Snf1-related kinase (SnRK) superfamily. The conserved Pseudomonas effector AvrPtoB acts as an E3 ubiquitin ligase and promotes bacterial virulence. In this study, we identified a member of the Arabidopsis SnRK family, SnRK2.8, which interacts with AvrPtoB in yeast and in planta. We showed that SnRK2.8 was required for AvrPtoB virulence functions, including facilitating bacterial colonization, suppression of callose deposition, and targeting the plant defense regulator NPR1 and analyses receptor FLS2. Mass spectrometry analysis revealed that AvrPtoB phosphorylation occurs at multiple serine residues in planta, with S258 phosphorylation significantly reduced in the snrk2.8 knockout. AvrPtoB phospho-null mutants exhibited compromised virulence functions and were unable to suppress NPR1 accumulation, FLS2 accumulation, or inhibit FLS2-BAK1 complex formation upon flagellin perception. Taken together, these data identify a conserved plant kinase utilized by a pathogen effector to promote disease.

Novel Aspects on The Interaction Between Grapevine and Plasmopara viticola: Dual-RNA-Seq Analysis Highlights Gene Expression Dynamics in The Pathogen and The Plant During The Battle For Infection

Mgaloblishvili, a Vitis vinifera cultivar, exhibits unique resistance traits against Plasmopara viticola, the downy mildew agent. This offers the unique opportunity of exploring the molecular responses in compatible and incompatible plant-pathogen interaction. In this study, whole transcriptomes of Mgaloblishvili, Pinot noir (a V. vinifera susceptible cultivar), and Bianca (a resistant hybrid) leaves, inoculated and non-inoculated with the pathogen, were used to identify P. viticola effector-encoding genes and plant susceptibility/resistance genes. Multiple effector-encoding genes were identified in P. viticola transcriptome, with remarkable expression differences in relation to the inoculated grapevine cultivar. Intriguingly, five apoplastic effectors specifically associated with resistance in V. vinifera. Gene coexpression network analysis identified specific modules and metabolic changes occurring during infection in the three grapevine cultivars. Analysis of these data allowed, for the first time, the detection in V. vinifera of a putative P. viticola susceptibility gene, encoding a LOB domain-containing protein. Finally, the de novo assembly of Mgaloblishvili, Pinot noir, and Bianca transcriptomes and their comparison highlighted novel candidate genes that might be at the basis of the resistant phenotype. These results open the way to functional analysis studies and to new perspectives in molecular breeding of grapevine for resistance to P. viticola.

Effect of temperature on Pi54-mediated leaf blast resistance in rice

Assessment of temperature effect on plant resistance against diseases has become essential under climate change scenario as temperature rise is anticipated to modify host resistance. To determine temperature influence on resistance gene, a pair of near-isogenic rice lines differing for the Pi54 resistance gene was assessed against leaf blast. Blast resistance was determined as the extent of infection efficiency (IE) and sporulation (SP) at suboptimal (22 °C and 32 °C) and optimal temperature (27 °C) of pathogen aggressiveness. Relative resistance for IE and SP was higher at suboptimal temperature as compared to that of optimal temperature. Maximum level of resistance was at 22 °C where higher levels of expression of Pi54 and defence-regulatory transcription factor WRKY45 were also noted. At 32 °C, although some level of resistance noted, but level of Pi54 and WRKY45 expression was too low, suggesting that resistance recorded at higher temperature was due to reduced pathogen aggressiveness. At the optimal temperature for pathogen aggressiveness, comparatively lower levels of Pi54 and WRKY45 expression suggest possible temperature-induced interruption of the defence processes. The variation in resistance patterns modulated by temperature is appeared to be due to pathogen's sensitivity to temperature that leads to varying levels of Pi54 gene activation. Quick and violent activity of the pathogen at optimal temperature came into sight for the interruption of defence process activated by Pi54 gene. Evaluation of blast resistance genes under variable temperature conditions together with weather data could be applied in screening rice genotypes for selection of resistance having resilience to temperature rise.

Magnesium Deficiency Induced Global Transcriptome Change in Citrus sinensis Leaves Revealed by RNA-Seq

Magnesium (Mg) deficiency is one of the major constraining factors that limit the yield and quality of agricultural products. Uniform seedlings of the Citrus sinensis were irrigated with Mg deficient (0 mM MgSO₄) and Mg sufficient (1 mM MgSO₄) nutrient solutions for 16 weeks. CO₂ assimilation, starch, soluble carbohydrates, TBARS content and H₂O₂ production were measured. Transcriptomic analysis of C. sinensis leaves was performed by Illumina sequencing. Our results showed that Mg deficiency decreased CO₂ assimilation, but increased starch, sucrose, TBARS content and H₂O₂ production in C. sinensis leaves. A total of 4864 genes showed differential expression in response to Mg deficiency revealed by RNA-Seq and the transcriptomic data were further validated by real-time quantitative PCR (RT-qPCR). Gene ontology (GO) enrichment analysis indicated that the mechanisms underlying Mg deficiency tolerance in C. sinensis may be attributed to the following aspects: (a) enhanced microtubule-based movement and cell cycle regulation; (b) elevated signal transduction in response to biotic and abiotic stimuli; (c) alteration of biological processes by tightly controlling phosphorylation especially protein phosphorylation; (d) down-regulation of light harvesting and photosynthesis due to the accumulation of carbohydrates; (e) up-regulation of cell wall remodeling and antioxidant system. Our results provide a comprehensive insight into the transcriptomic profile of key components involved in the Mg deficiency tolerance in C. sinensis and enrich our understanding of the molecular mechanisms by which plants adapted to a Mg deficient condition.

Ergosterol, an orphan fungal microbe-associated molecular pattern (MAMP)

Fungal pathogens continue to pose a significant threat to crop production and food supply. The early stages of plant-fungus interactions are mostly mediated by microbe-associated molecular pattern (MAMP) molecules, perceived by plant pattern recognition receptors (PRRs). Currently, the identified fungal MAMP molecules include chitin, chitosan, β-glucans, elicitins and ergosterol. Although the molecular battles between host plants and infecting fungal phytopathogens have been studied extensively, many aspects still need to be investigated to obtain a holistic understanding of the intrinsic mechanisms, which is paramount in combating fungal plant diseases. Here, an overview is given of the most recent findings concerning an 'orphan' fungal MAMP molecule, ergosterol, and we present what is currently known from a synopsis of different genes, proteins and metabolites found to play key roles in induced immune responses in plant-fungus interactions. Clearly, integrative investigations are still needed to provide a comprehensive systems-based understanding of the dynamics associated with molecular mechanisms in plant-ergosterol interactions and associated host responses.

Knockout of AtMKK1 enhances salt tolerance and modifies metabolic activities in Arabidopsis

Mitogen-activated protein kinase (MAPK) pathways represent a crucial regulatory mechanism in plant development. The ability to activate and inactivate MAPK pathways rapidly in response to changing conditions helps plants to adapt to a changing environment. AtMKK1 is a stress response kinase that is capable of activating the MAPK proteins AtMPK3, AtMPK4 and AtMPK6. To elucidate its mode of action further, several tests were undertaken to examine the response of AtMKK1 to salt stress using a knockout (KO) mutant of AtMKK1. We found that AtMKK1 mutant plants tolerated elevated levels of salt during both germination and adulthood. Proteomic analysis indicated that the level of the α subunit of mitochrondrial H(+)-ATPase, mitochrondial NADH dehydrogenase and mitochrondrial formate dehydrogenase was enhanced in AtMKK1 knockout mutants upon high salinity stress. The level of formate dehydrogenase was further confirmed by immunoblotting and enzyme assay. The possible involvement of these enzymes in salt tolerance is discussed.

Phosphorylation of intrinsically disordered regions in remorin proteins

Plant-specific remorin proteins reside in subdomains of plasma membranes, originally termed membrane rafts. They probably facilitate cellular signal transduction by direct interaction with signaling proteins such as receptor-like kinases and may dynamically modulate their lateral segregation within plasma membranes. Recent evidence suggests such functions of remorins during plant-microbe interactions and innate immune responses, where differential phosphorylation of some of these proteins has been described to be dependent on the perception of the microbe-associated molecular pattern (MAMP) flg22 and the presence of the NBS-LRR resistance protein RPM1. A number of specifically phosphorylated residues in their highly variable and intrinsically disordered N-terminal regions have been identified. Sequence diversity of these evolutionary distinct domains suggests that remorins may serve a wide range of biological functions. Here, we describe patterns and features of intrinsic disorder in remorin protein and discuss possible functional implications of phosphorylation within these rapidly evolving domains.

Regulatory subunit B'gamma of protein phosphatase 2A prevents unnecessary defense reactions under low light in Arabidopsis

Light is an important environmental factor that modulates acclimation strategies and defense responses in plants. We explored the functional role of the regulatory subunit B'γ (B'γ) of protein phosphatase 2A (PP2A) in light-dependent stress responses of Arabidopsis (Arabidopsis thaliana). The predominant form of PP2A consists of catalytic subunit C, scaffold subunit A, and highly variable regulatory subunit B, which determines the substrate specificity of PP2A holoenzymes. Mutant leaves of knockdown pp2a-b'γ plants show disintegration of chloroplasts and premature yellowing conditionally under moderate light intensity. The cell-death phenotype is accompanied by the accumulation of hydrogen peroxide through a pathway that requires CONSTITUTIVE EXPRESSION OF PR GENES5 (CPR5). Moreover, the pp2a-b'γ cpr5 double mutant additionally displays growth suppression and malformed trichomes. Similar to cpr5, the pp2a-b'γ mutant shows constitutive activation of both salicylic acid- and jasmonic acid-dependent defense pathways. In contrast to cpr5, however, pp2a-b'γ leaves do not contain increased levels of salicylic acid or jasmonic acid. Rather, the constitutive defense response associates with hypomethylation of DNA and increased levels of methionine-salvage pathway components in pp2a-b'γ leaves. We suggest that the specific B'γ subunit of PP2A is functionally connected to CPR5 and operates in the basal repression of defense responses under low irradiance.

MAPK machinery in plants: recognition and response to different stresses through multiple signal transduction pathways

The mitogen-activated protein kinase (MAPK) cascades play diverse roles in intra- and extra-cellular signaling in plants. MAP kinases are the component of kinase modules which transfer information from sensors to responses in eukaryotes including plants. They play a pivotal role in transduction of diverse extracellular stimuli such as biotic and abiotic stresses as well as a range of developmental responses including differentiation, proliferation and death. Several cascades are induced by different biotic and abiotic stress stimuli such as pathogen infections, heavy metal, wounding, high and low temperatures, high salinity, UV radiation, ozone, reactive oxygen species, drought and high or low osmolarity. MAPK signaling has been implicated in biotic stresses and has also been associated with hormonal responses. The cascade is regulated by various mechanisms, including not only transcriptional and translational regulation but through post-transcriptional regulation such as protein-protein interactions. Recent detailed analysis of certain specific MAP kinase pathways have revealed the specificity of the kinases in the cascade, signal transduction patterns, identity of pathway targets and the complexity of the cascade. The latest insights and finding are discussed in this paper in relation to the role of MAPK pathway modules in plant stress signaling.

Quantitative phosphoproteomics of tomato mounting a hypersensitive response reveals a swift suppression of photosynthetic activity and a differential role for hsp90 isoforms

An important mechanism by which plants defend themselves against pathogens is the rapid execution of a hypersensitive response (HR). Tomato plants containing the Cf-4 resistance gene mount an HR that relies on the activation of phosphorylation cascades, when challenged with the Avr4 elicitor secreted by the pathogenic fungus Cladosporium fulvum. Phosphopeptides were isolated from tomato seedlings expressing both Cf-4 and Avr4 using titanium dioxide columns and LC-MS/MS analysis led to the identification of 50 phosphoproteins, most of which have not been described in tomato before. Phosphopeptides were quantified using a label-free approach based on the MS peak areas. We identified 12 phosphopeptides for which the abundance changed upon HR initiation, as compared to control seedlings. Our results suggest that photosynthetic activity is specifically suppressed in a phosphorylation-dependent way during the very early stages of HR development. In addition, phosphopeptides originating from four Hsp90 isoforms exhibited altered abundances in Cf-4/Avr4 seedlings compared to control seedlings, suggesting that the isoforms of this chaperone protein have a different function in defense signaling. We show that label-free relative quantification of the phosphoproteome of complex samples is feasible, allowing extension of our knowledge on the general physiology and defense signaling of plants mounting the HR.

Plant-pathogen interactions: what is proteomics telling us?

Over the years, several studies have been performed to analyse plant-pathogen interactions. Recently, functional genomic strategies, including proteomics and transcriptomics, have contributed to the effort of defining gene and protein function and expression profiles. Using these 'omic' approaches, pathogenicity- and defence-related genes and proteins expressed during phytopathogen infections have been identified and enormous datasets have been accumulated. However, the understanding of molecular plant-pathogen interactions is still an intriguing area of investigation. Proteomics has dramatically evolved in the pursuit of large-scale functional assignment of candidate proteins and, by using this approach, several proteins expressed during phytopathogenic interactions have been identified. In this review, we highlight the proteins expressed during plant-virus, plant-bacterium, plant-fungus and plant-nematode interactions reported in proteomic studies, and discuss these findings considering the advantages and limitations of current proteomic tools.

Post-translational modification of host proteins in pathogen-triggered defence signalling in plants

Microbial plant pathogens impose a continuous threat to global food production. Similar to animals, an innate immune system allows plants to recognize pathogens and swiftly activate defence. To activate a rapid response, receptor-mediated pathogen perception and subsequent downstream signalling depends on post-translational modification (PTM) of components essential for defence signalling. We discuss different types of PTMs that play a role in mounting plant immunity, which include phosphorylation, glycosylation, ubiquitination, sumoylation, nitrosylation, myristoylation, palmitoylation and glycosylphosphatidylinositol (GPI)-anchoring. PTMs are rapid, reversible, controlled and highly specific, and provide a tool to regulate protein stability, activity and localization. Here, we give an overview of PTMs that modify components essential for defence signalling at the site of signal perception, during secondary messenger production and during signalling in the cytoplasm. In addition, we discuss effectors from pathogens that suppress plant defence responses by interfering with host PTMs.

Phosphorylation analysis of plant viral proteins

Posttranslational modification of proteins is a key regulatory mechanism in a variety of cellular processes. This chapter outlines the concepts and methods used to investigate protein phosphorylation and its physiological relevance during plant virus infection. Rather than providing an exhaustive review of the experimental protocols for protein phosphorylation analysis, we focus on methods that can be used to study phosphorylation of viral proteins. We address the following points: how to determine that a viral protein of interest is phosphorylated; how to map the phosphorylation sites; how to identify the protein kinase(s) involved. Finally, we describe a number of useful strategies to evaluate the biological significance of phosphorylation.

A novel rice MAPK gene, OsBIMK2, is involved in disease-resistance responses

The mitogen-activated protein kinase (MAPK) cascades play important roles in transmission of extracellular signals to the downstream effector proteins through a mechanism of protein phosphorylation. In this study, we isolated and identified a novel rice MAPK gene, OSBIMK2 ( ORYZAE SATIVA L. BTH-Induced MAP Kinase 2). The OSBIMK2 encodes a 506 amino acid protein with molecular weight of 63 kD. The recombinant OSBIMK2 expressed in ESCHERICHIA COLI showed an autophosphorylation activity IN VITRO. OSBIMK2 is a single-copy gene in the rice genome. Expression of OSBIMK2 was activated upon treatment with benzothiadiazole (BTH), which is capable of inducing disease resistance in rice. Expression of OsBIMK2 was also up-regulated during early stage after inoculation with MAGNAPORTHE GRISEA in BTH-treated rice seedlings and during an incompatible interaction between M. GRISEA and a blast-resistant rice genotype. Over-expression of the rice OSBIMK2 gene in transgenic tobacco resulted in an enhanced disease resistance against tomato mosaic virus and a fungal pathogen, ALTERNARIA ALTERNATA. These results suggest that OSBIMK2 plays a role in disease resistance responses.

The role of mass spectrometry in plant systems biology

Large-scale analyses of proteins and metabolites are intimately bound to advancements in MS technologies. The aim of these non-targeted "omic" technologies is to extend our understanding beyond the analysis of only parts of the system. Here, metabolomics and proteomics emerged in parallel with the development of novel mass analyzers and hyphenated techniques such as gas chromatography coupled to time-of-flight mass spectrometry (GC-TOF-MS) and multidimensional liquid chromatography coupled to mass spectrometry (LC-MS). The analysis of (i) proteins (ii) phosphoproteins, and (iii) metabolites is discussed in the context of plant physiology and environment and with a focus on novel method developments. Recently published studies measuring dynamic (quantitative) behavior at these levels are summarized; for these works, the completely sequenced plants Arabidopsis thaliana and Oryza sativa (rice) have been the primary models of choice. Particular emphasis is given to key physiological processes such as metabolism, development, stress, and defense. Moreover, attempts to combine spatial, tissue-specific resolution with systematic profiling are described. Finally, we summarize the initial steps to characterize the molecular plant phenotype as a corollary of environment and genotype.

Molecular characterization of the ZKT gene encoding a protein with PDZ, K-Box, and TPR motifs in Arabidopsis

The ZKT gene from Arabidopsis encodes a polypeptide of 335 amino acid residues, with a calculated molecular mass of 37.4 kDa. ZKT is a member of a novel protein family present in the plant kingdom, which contains a PDZ, a K-box, and a TPR motif. A BLAST search indicated that the ZKT gene is a single gene in Arabidopsis and that ZKT homologs are present in soybean and rice but not in animals. The level of ZKT mRNA decreased after wounding. Antisera from rabbit immunized with recommbinant ZKT protein recognized a protein of 37 kDa in Arabidopsis. Western analysis with anti-ZKT antibody indicated that the level of ZKT protein does not change after wounding. The ZKT protein has consensus sequence motifs for phosphorylation. Immunoprecipitation with anti-ZKT antibody and western analysis with anti-phosphoamino acid antibody indicated that the ZKT protein is phosophorylated at the threonine and serine residues after wounding. These results suggest that the ZKT protein may act as a molecular adaptor regulated by phosphorylation in wound responses.

Plant-specific calmodulin-binding proteins

Calmodulin CaM is the most prominent Ca2+ transducer in eukaryotic cells, regulating the activity of numerous proteins with diverse cellular functions. Many features of CaM and its downstream targets are similar in plants and other eukaryotes. However, plants possess a unique set of CaM-related proteins, and several unique CaM target proteins. This review discusses recent progress in identifying plant-specific CaM-binding proteins and their roles in response to biotic and abiotic stresses and development. The review also addresses aspects emerging from recent structural studies of CaM interactions with target proteins relevant to plants.

Protein phosphorylation in Nicotiana tabacum cells in response to perception of lipopolysaccharides from Burkholderia cepacia

Bacterial LPS have the ability to act as modulators of the innate immune response in plants. Complex and largely unresolved perception systems exist for LPS on the plant cell surfaces that lead to the activation of multiple intracellular defense signaling pathways. The aim of the present study was to investigate the perception mechanism of cultured Nicotiana tabacum cells towards LPS from Burkholderia cepacia (LPS(B.cep.)), with regard to the role of protein phosphorylation during signal perception-related responses to gain a better understanding of the chemosensory perception of LPS elicitor signals in plant cells. In vivo labeling of protein phosphorylation events during signal transduction indicated the rapid phosphorylation of several proteins with the hyperphosphorylation of two proteins of 28 and 2 kDa, respectively. Significant differences and de novo LPS-induced phosphorylation were also observed with two-dimensional analysis. The protein kinase inhibitor, staurosporine, totally inhibited the extracellular alkalinization response induced by LPS(B.cep.), while the oxidative burst was only partially inhibited by staurosporine. Inhibition of protein phosphatase activity by calyculin A intensified the LPS(B.cep.) responses. The results indicate that perception- and signal transduction responses during LPS(B.cep.) elicitation of tobacco cells require a balance between the actions of certain protein kinases and protein phosphatases.

Virus-induced silencing of WIPK and SIPK genes reduces resistance to a bacterial pathogen, but has no effect on the INF1-induced hypersensitive response (HR) in Nicotiana benthamiana

Activation of two mitogen-activated protein kinases (MAPKs), wound-induced protein kinase (WIPK) and salicylic acid-induced protein kinase (SIPK), is one of the earliest responses that occur in tobacco plants that have been wounded, treated with pathogen-derived elicitors or challenged with avirulent pathogens. We isolated cDNAs for these MAPKs (NbWIPKand NbSIPK) from Nicotiana benthamiana. The function of NbWIPK and NbSIPK in mediating the hypersensitive response (HR) triggered by infiltration with INF1 protein (the major elicitin secreted by Phytophthora infestans), and the defense response to an incompatible bacterial pathogen (Pseudomonas cichorii), was investigated by employing virus-induced gene silencing (VIGS) to inhibit expression of the WIPK and SIPK genes in N. benthamiana. Silencing of WIPK or SIPK, or both genes simultaneously, resulted in reduced resistance to P. cichorii, but no change was observed in the timing or extent of HR development after treatment with INF1.

Identification of 14 new phosphoproteins involved in important plant mitochondrial processes

Protein phosphorylation is a very important posttranslational modification the role of which is practically unexplored in mitochondria. Using two-dimensional gel electrophoresis followed by mass spectrometry, 14 new phosphoproteins are identified in potato tuber mitochondria, all household proteins also present in mammalian and fungal mitochondria. Seven of the new phosphoproteins are involved in the tricarboxylic acid cycle or associated reactions, four are subunits of respiratory complexes and involved in electron transport, ATP synthesis and protein processing, two are heat shock proteins and one is involved in defence against oxidative stress. These findings open up entirely new possibilities for the regulation and signal integration of mitochondrial processes.

Strategies for structural proteomics of prokaryotes: Quantifying the advantages of studying orthologous proteins and of using both NMR and X-ray crystallography approaches

Only about half of non-membrane-bound proteins encoded by either bacterial or archaeal genomes are soluble when expressed in Escherichia coli (Yee et al., Proc Natl Acad Sci USA 2002;99:1825-1830; Christendat et al., Prog Biophys Mol Biol 200;73:339-345). This property limits genome-scale functional and structural proteomics studies, which depend on having a recombinant, soluble version of each protein. An emerging strategy to increase the probability of deriving a soluble derivative of a protein is to study different sequence homologues of the same protein, including representatives from thermophilic organisms, based on the assumption that the stability of these proteins will facilitate structural analysis. To estimate the relative merits of this strategy, we compared the recombinant expression, solubility, and suitability for structural analysis by NMR and/or X-ray crystallography for 68 pairs of homologous proteins from E. coli and Thermotoga maritima. A sample suitable for structural studies was obtained for 62 of the 68 pairs of homologs under standardized growth and purification procedures. Fourteen (eight E. coli and six T. maritima proteins) samples generated NMR spectra of a quality suitable for structure determination and 30 (14 E. coli and 16 T. maritima proteins) samples formed crystals. Only three (one E. coli and two T. maritima proteins) samples both crystallized and had excellent NMR properties. The conclusions from this work are: (1) The inclusion of even a single ortholog of a target protein increases the number of samples for structural studies almost twofold; (2) there was no clear advantage to the use of thermophilic proteins to generate samples for structural studies; and (3) for the small proteins analyzed here, the use of both NMR and crystallography approaches almost doubled the number of samples for structural studies.