Correction: Enterovirus 71 Protease 2Apro Targets MAVS to Inhibit Anti-Viral Type I Interferon Responses.

[This corrects the article DOI: 10.1371/journal.ppat.1003231.].

Hepatitis C virus induces oxidation and degradation of apolipoprotein B to enhance lipid accumulation and promote viral production.

Hepatitis C virus (HCV) infection induces the degradation and decreases the secretion of apolipoprotein B (ApoB). Impaired production and secretion of ApoB-containing lipoprotein is associated with an increase in hepatic steatosis. Therefore, HCV infection-induced degradation of ApoB may contribute to hepatic steatosis and decreased lipoprotein secretion, but the mechanism of HCV infection-induced ApoB degradation has not been completely elucidated. In this study, we found that the ApoB level in HCV-infected cells was regulated by proteasome-associated degradation but not autophagic degradation. ApoB was degraded by the 20S proteasome in a ubiquitin-independent manner. HCV induced the oxidation of ApoB via oxidative stress, and oxidized ApoB was recognized by the PSMA5 and PSMA6 subunits of the 20S proteasome for degradation. Further study showed that ApoB was degraded at endoplasmic reticulum (ER)-associated lipid droplets (LDs) and that the retrotranslocation and degradation of ApoB required Derlin-1 but not gp78 or p97. Moreover, we found that knockdown of ApoB before infection increased the cellular lipid content and enhanced HCV assembly. Overexpression of ApoB-50 inhibited lipid accumulation and repressed viral assembly in HCV-infected cells. Our study reveals a novel mechanism of ApoB degradation and lipid accumulation during HCV infection and might suggest new therapeutic strategies for hepatic steatosis.

Slow stripe rusting in Chinese wheat Jimai 44 conferred by Yr29 in combination with a major QTL on chromosome arm 6AL.

KEY MESSAGE: YrJ44, a more effective slow rusting gene than Yr29, was localized to a 3.5-cM interval between AQP markers AX-109373479 and AX-109563479 on chromosome 6AL. "Slow rusting" (SR) is a type of adult plant resistance (APR) that can provide non-specific durable resistance to stripe rust in wheat. Chinese elite wheat cultivar Jimai 44 (JM44) has maintained SR to stripe rust in China since its release despite exposure to a changing and variable pathogen population. An F2:6 population comprising 295 recombinant inbred lines (RILs) derived from a cross between JM44 and susceptible cultivar Jimai 229 (JM229) was used in genetic analysis of the SR. The RILs and parental lines were evaluated for stripe rust response in five field environments and genotyped using the Affymetrix Wheat55K SNP array and 13 allele-specific quantitative PCR-based (AQP) markers. Two stable QTL on chromosome arms 1BL and 6AL were identified by inclusive composite interval mapping. The 1BL QTL was probably the pleiotropic gene Lr46/Yr29/Sr58. QYr.nwafu-6AL (hereafter named YrJ44), mapped in a 3.5-cM interval between AQP markers AX-109373479 and AX-109563479, was more effective than Yr29 in reducing disease severity and relative area under the disease progress curve (rAUDPC). RILs harboring both YrJ44 and Yr29 displayed levels of SR equal to the resistant parent JM44. The AQP markers linked with YrJ44 were polymorphic and significantly correlated with stripe rust resistance in a panel of 1,019 wheat cultivars and breeding lines. These results suggested that adequate SR resistance can be obtained by combining YrJ44 and Yr29 and the AQP markers can be used in breeding for durable stripe rust resistance.

Improved Electronic Structure from Spin-State Reconstruction of a Heteronuclear Fe-Co Diatomic Pair to Boost the Fenton-like Reaction.

Dual-atom catalysts (DACs) are promising candidates for various catalytic reactions, including electrocatalysis, chemical synthesis, and environmental remediation. However, the high-activity origin and mechanism underlying intrinsic activity enhancement remain elusive, especially for the Fenton-like reaction. Herein, we systematically compared the catalytic performance of dual-atom FeCo-N/C with its single-atom counterparts by activating peroxymonosulfate (PMS) for pollutant abatement. The unusual spin-state reconstruction on FeCo-N/C is demonstrated to effectively improve the electronic structure of Fe and Co in the d orbital and enhance the PMS activation efficiency. Accordingly, the dual-atom FeCo-N/C with an intermediate-spin state remarkably boosts the Fenton-like reaction by almost 1 order of magnitude compared with low-spin Co-N/C and high-spin Fe-N/C. Moreover, the established dual-atom-activated PMS system also exhibits excellent stability and robust resistance against harsh conditions. Combined theoretical calculations reveal that unlike unitary Co atom or Fe atom transferring electrons to the PMS molecule, the Fe atom of FeCo-N/C provides extra electrons to the neighboring Co atom and positively shifts the d band of the Co center, thereby optimizing the PMS adsorption and decomposition into a unique high-valent FeIV-O-CoIV species via a low-energy barrier pathway. This work advances a conceptually novel mechanistic understanding of the enhanced catalytic activity of DACs in Fenton-like reactions and helps to expand the application of DACs in various catalytic reactions.

Performance optimization and mechanism analysis of applied Enteromorpha-based composite dust suppressant.

In order to solve the problem of environmental pollution caused by the escape of coal dust in open-pit coal mines, a composite dust suppressant was prepared from Enteromorpha, and the preparation factors (water-soluble polymer, temperature, solid content and surfactant) were optimized. The mechanism of dust suppression and the possibility of large-scale field application were discussed. The research results on the related properties of dust suppressants showed that the performance of Enteromorpha-based dust suppressants prepared by this method was excellent compared with similar studies. Among them, polyacrylamide (PAM) Enteromorpha-based dust suppressant had the best performance, with viscosity of 25.1 mPa s and surface tension of 27.05 mN/m. Moreover, PAM Enteromorpha-based dust suppressant had the best effect, with the mass loss of 2.94% under the wind speed of 10 m/s and the coal dust loss rate of 4.6% after rain erosion, and it had strong water retention performance. Through the discussion of dust suppression mechanism, it was found that the mechanical entangled network structure with hydrogen bonds as nodes was formed after the graft copolymerization of PAM and Enteromorpha. It had high permeability and good adhesion. After quickly wetting coal dust, it formed a dense package for coal dust. The field experiment also showed that the use of Enteromorpha-based dust suppressant can effectively inhibit the escape of coal dust. From the point of view of economy and efficiency, Enteromorpha can save 30% of the material cost and the dust suppression efficiency can reach 89-94%. Therefore, the Enteromorpha-based dust suppressant may stably suppress coal dust on the basis of reducing the cost.

Effects of the different waxy proteins on starch biosynthesis, starch physicochemical properties and Chinese noodle quality in wheat.

Noodles are an important food in Asia. Wheat starch is the most important component in Chinese noodles. Loss of the waxy genes leads to lower activity of starch synthesis enzymes and decreased amylose content that further affects starch properties and noodle quality. To study the effects of different waxy (Wx) protein subunits on starch biosynthesis and processing quality, the high-yielding wheat cultivar Jimai 22 was treated with the mutagen ethyl methane sulfonate (EMS) to produce a population of Wx lines and chosen 7 Wx protein combinations. The amylose content increased but swelling power decreased as the number of Wx proteins increased. Both GBSS activity and gene expression were the lowest for the waxy mutant, followed by the mutants with 1 Wx protein. The combinations of these mutant alleles lead to reductions in both RNA expression and protein levels. Noodles made from materials with 2 Wx protein subunits had the highest score, which agreed with peak viscosity. The influence of the Wx-B1 protein on amylose synthesis and noodle quality was the highest, whereas the influence of Wx-A1 protein was the lowest. Mutants with lower amylose content caused by the absence of 1 subunit, especially the Wx-B1 subunit, had superior noodle quality. Additionally, the identified mutant lines can be used as intermediate materials to improve wheat quality. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-022-01292-x.

Synthesis, Herbicidal Activity and Toxicity Evaluation of Secondary Ammonium Salts from Turpentine Oil for Sustainable Weed Control.

Three series of secondary ammonium chloride from turpentine were synthesized and evaluated as botanical herbicides. The preemergence herbicidal activities against ryegrass (Loliun multiflorum) and barnyard grass (Echinochloa crus-galli) were investigated using water as the only solvent. Their toxicity was evaluated by cytotoxicity assays. Preliminary results demonstrated that the herbicidal performance of the prepared salts was similar or much higher than that of corresponding secondary amines and even commercial herbicide glyphosate. Promisingly, compound 14e containing a cyclohexyl-substituted p-menthene skeleton with an IC50 value of 0.0014 mM against root growth of ryegrass showed 39-fold higher herbicidal activity than glyphosate. Besides, this compound was found to be nontoxic to human and animal cells, indicating the potential application as a water-soluble herbicide for ryegrass control.

Chemokine (C-X-C Motif) Ligand 4 Is a Restrictor of Respiratory Syncytial Virus Infection and an Indicator of Clinical Severity.

Rationale: Respiratory syncytial virus (RSV) is the leading cause of childhood respiratory infections worldwide; however, no vaccine is available, and treatment options are limited. Identification of host factors pivotal to viral replication may inform the development of novel therapies, prophylaxes, or diagnoses.Objectives: To identify host factors involved in RSV replication and to evaluate their potential for disease management.Methods: A gain-of-function screening was performed on the basis of a genome-wide human complementary DNA library screen for host factors involved in RSV replication. The antiviral mechanism of CXCL4 (chemokine [C-X-C motif] ligand 4) was analyzed. Its clinical role was evaluated via nasopharyngeal aspirates and plasma samples from patients with RSV infection and different disease severities.Measurements and Main Results: Forty-nine host factors restricting RSV replication were identified by gain-of-function screening, with CXCL4 showing the strongest antiviral effect, which was secretion dependent. CXCL4 blocked viral attachment through binding to the RSV main receptor heparan sulfate, instead of through interacting with RSV surface proteins. Intranasal pretreatment with CXCL4 alleviated inflammation in RSV-infected mice, as shown by decreased concentrations of tumor necrosis factor and viral load in BAL fluid samples as well as by viral nucleocapsid protein histological staining in lungs. Compared with non-RSV infections, RSV infections induced elevated CXCL4 concentrations both in plasma and airway samples from mice and pediatric patients. The airway CXCL4 concentration was correlated with viral load and disease severity in patients (P < 0.001).Conclusions: Our results suggest that CXCL4 is an RSV restriction factor that can block viral entry and serve as an indicator of clinical severity in RSV infections.

Synthesis and biological activity of pyridine acylhydrazone derivatives of isopimaric acid.

Pyridine acylhydrazone derivatives of isopimaric acid were synthesized and characterized. The minimum inhibitory concentrations of the compounds against five bacteria were determined and most of the compounds displayed some degree of antibacterial activity. The results showed that antimicrobial activity against Streptococcus pneumoniae improved when halogen atoms were introduced into the isopimaric acid, especially when one bromine atom was introduced in the para-position of isopimaric acid. Compound isopimaric acid (5-bromo pyridine-2-formaldehyde) acylhydrazone exhibited a significant antitumorial activity against hepatocarcioma cells (HepG-2) and breast cancer cells (MDA-MB-231), with inhibition degrees of 74.21% and 70.39%, respectively, at 100 µM.[Formula: see text].

Determination of monosaccharides hydrolyzed from polysaccharides in activated sludge by ion chromatography-mass spectrometry with online pretreatment of column switching technique.

The simultaneous determination of monosaccharides present in the activated sludge would be crucial to understand the water treatment mechanism. Herein, an ion chromatography-mass spectrometry (IC-MS) with online pretreatment of column switching technique was proposed to analyze monosaccharides hydrolyzed from extracellular polysaccharides in the activated sludge. When the matrix was eliminated in the first dimension, monosaccharides were immediately identified by IC-MS. The improved ionization efficiency was achieved with the addition of T-joint prior to MS. During the performance test, our established method showed excellent detection limits ranging from 0.34 to 2.15 µg/L for all sugar targets. Great linearity (R ≥ 0.9955) was also achieved using this method in the range from 0.01 to 5 mg/L. Furthermore, the average recoveries were obtained between 84.82 and 113.46%. RSDs for peak areas and retention times were determined as 3.76% and 0.27%, respectively. Finally, this approach provided a rapid, convenient, and practical determination of monosaccharides in the activated sludge, which would be helpful for the analysis of monosaccharides derived from other biological samples.

Variants of the phenylalanine hydroxylase gene in neonates with phenylketonuria in Hainan, China.

OBJECTIVE: To investigate the incidence of phenylalanine hydroxylase (PAH) deficiency and PAH genotypes in neonates in Hainan, China. Methods: We performed heal stick to collect blood and obtain dry blood spot specimens from newborns in Hainan from January 2007 to December 2016. Phenylalanine (Phe) concentration in these dry blood spots was measured by the fluorescence method to screen phenylketonuria (PKU). For suspicious samples, the genotypes of the PAH gene were amplified by biotin labeled oligonucleotide primers. Polymerase chain reaction (PCR) products were then analyzed by flow-through hybridization to detect genotypes. At the same time, peripheral blood samples of children suspicious of PKU and their parents were used to perform gene sequencing. Results: Of the 914,520 newborns screened, 29 of them had PAH deficiency. The incidence of PAH deficiency in Hainan was 3.17/100,000. A total of 58 mutant alleles belonging to 15 different types were identified in the 29 patients. In terms of genotypes frequency, the top 4 were: c.611A > G 20.7% (12/58) , c.728G > A 17.2%, c.158G > A 15.2% (9/58) and c.721C > T 13.8% (8/58). The frequencies of other genotypes were all below 10%. Conclusion: The incidence of PAH deficiency in Hainan is relatively high among all provinces in southern China. With a total frequency of 67.2%, c.611A > G, c.728G > A, c.158G > A and c.721C > T, and are the most common PAH gene genotypes.

Genome-wide analysis and identification of the low potassium stress responsive gene SiMYB3 in foxtail millet (Setariaitalica L.).

BACKGROUND: Potassium (K) is essential to plant growth and development. Foxtail millet (Setaria italic L.) is an important fodder grain crop in arid and semi-arid regions of Asia and Africa because of its strong tolerance to drought and barren stresses. The molecular mechanisms of physiological and biochemical responses and regulations to various abiotic stresses such as low potassium conditions in foxtail millet are not fully understood, which hinders the research and exploitation of this valuable resource. RESULTS: In this research, we demonstrated that the millet variety Longgu 25 was the most insensitive variety to low potassium stress among other five varieties. The transcriptome analysis of Longgu 25 variety revealed a total of 26,192 and 26,849 genes from the K+-deficient and normal transcriptomic libraries by RNA-seq, respectively. A total of 1982 differentially expressed genes (DEGs) were identified including 866 up-regulated genes and 1116 down-regulated genes. We conducted a comparative analysis of these DEGs under low-K+ stress conditions and discovered 248 common DEGs for potassium deprivation among foxtail millet, rice and Arabidopsis. Further Gene Ontology (GO) enrichment analysis identified a series of candidate genes that may involve in K+-deficient response and in intersection of molecular functions among foxtail millet, rice and Arabidopsis. The expression profiles of randomly selected 18 candidate genes were confirmed as true DEGs with RT-qPCR. Furthermore, one of the 18 DEGs, SiMYB3, is specifically expressed only in the millet under low-K+ stress conditions. Overexpression of SiMYB3 promoted the main root elongation and improved K+ deficiency tolerance in transgenic Arabidopsis plants. The fresh weight of the transgenic plants was higher, the primary root length was longer and the root surface-area was larger than those of control plants after K+ deficiency treatments. CONCLUSIONS: This study provides a global view of transcriptomic resources relevant to the K+-deficient tolerance in foxtail millet, and shows that SiMYB3 is a valuable genetic resource for the improvement of K+ deficiency tolerance in foxtail millet.

Transduction with Lentiviral Vectors Altered the Expression Profile of Host MicroRNAs.

RNA interference (RNAi) is widely used in gene knockdown analysis and as a tool to screen host genes involved in viral infection. Owing to the limitations of transducing cells with synthetic small interfering RNAs (siRNAs), lentiviral short hairpin RNA (shRNA) vectors are more widely used. However, we found that stable transduction with lentiviral shRNA vectors inhibited hepatitis C virus (HCV) propagation in human hepatoma cells. We found by microRNA (miRNA) microarray analysis that this inhibition was induced by the alteration of host miRNA expression. In addition to one miRNA (miR-196b-5p) previously reported to be involved in HCV infection, other miRNAs (miR-216a-5p, -216b-5p, 217, and -30b-5p) were found to influence HCV infection in this study. Further studies suggested that this effect was independent of the transcription of shRNAs. The lentiviral vector itself and the integration site of the lentiviral vector might determine the change in miRNA expression. Moreover, the upregulation of JUN contributed to the dysregulation of miR-216a-5p, -216b-5p, and -217 in stably transduced cells. Although the changes in miRNA expression were beneficial for inhibiting HCV infection in our study, this off-target effect should be considered when transduction with lentiviral vectors is performed for other purposes, especially in therapy.IMPORTANCE We found that stable transduction with lentiviral shRNA was able to nonspecifically inhibit HCV infection by the dysregulation of host miRNAs. Previous studies showed that the overexpression of shRNAs oversaturated the host miRNA pathways to inhibit HCV infection. In contrast, the miRNA machinery was not affected in our study. Knockout studies suggested that the nonspecific effect was independent of the transcription of shRNAs. The lentiviral vector itself and the integration sites in the host genome determined the changes in miRNAs. Stable transduction with lentiviral vectors was able to increase the expression of JUN, which in turn upregulated miR-216a-5p, miR-216b-5p, and miR-217. miR-216a-5p and miR-216b-5p might inhibit HCV by suppressing the host autophagic machinery. Our study suggested a novel nonspecific effect of lentiviral vectors, and this side effect should be considered when transduction with lentiviral vectors is performed for other purposes, especially in therapy.

Correction: Enterovirus 71 Protease 2Apro Targets MAVS to Inhibit Anti-Viral Type I Interferon Responses.

[This corrects the article DOI: 10.1371/journal.ppat.1003231.].

Enterovirus 71 protease 2Apro and 3Cpro differentially inhibit the cellular endoplasmic reticulum-associated degradation (ERAD) pathway via distinct mechanisms, and enterovirus 71 hijacks ERAD component p97 to promote its replication.

Endoplasmic reticulum-associated degradation (ERAD) is an important function for cellular homeostasis. The mechanism of how picornavirus infection interferes with ERAD remains unclear. In this study, we demonstrated that enterovirus 71 (EV71) infection significantly inhibits cellular ERAD by targeting multiple key ERAD molecules with its proteases 2Apro and 3Cpro using different mechanisms. Ubc6e was identified as the key E2 ubiquitin-conjugating enzyme in EV71 disturbed ERAD. EV71 3Cpro cleaves Ubc6e at Q219G, Q260S, and Q273G. EV71 2Apro mainly inhibits the de novo synthesis of key ERAD molecules Herp and VIMP at the protein translational level. Herp differentially participates in the degradation of different glycosylated ERAD substrates α-1 antitrypsin Null Hong Kong (NHK) and the C-terminus of sonic hedgehog (SHH-C) via unknown mechanisms. p97 was identified as a host factor in EV71 replication; it redistributed and co-exists with the viral protein and other known replication-related molecules in EV71-induced replication organelles. Electron microscopy and multiple-color confocal assays also showed that EV71-induced membranous vesicles were closely associated with the endoplasmic reticulum (ER), and the ER membrane molecule RTN3 was redistributed to the viral replication complex during EV71 infection. Therefore, we propose that EV71 rearranges ER membranes and hijacks p97 from cellular ERAD to benefit its replication. These findings add to our understanding of how viruses disturb ERAD and provide potential anti-viral targets for EV71 infection.

[Analysis of inborn error metabolism in 277 children with autism spectrum disorders from Hainan].

OBJECTIVE: To assess the value of dry blood spot tandem mass spectrometry for the diagnosis of autism spectrum disorder (ASD). METHODS: Peripheral blood samples of 277 autistic children were collected. Their amino acid and carnitine profiles were detected by liquid chromatography tandem mass spectrometry. Urine samples of suspected patients were collected for verification by gas chromatography mass spectrometry. Blood samples were also taken for genetic testing. RESULTS: Of the 277 children with ASD, 19 (6.9%) were suspected to be with inborn error of metabolism (IEM), which included 6 cases with amino acidemia, 9 with organic acidemia and 4 with fatty acidemia. Three cases of phenylketonuria, one case of homocysteinemia, one case of propionemia, one case of methylmalonic acidemia, one case of glutaric acidemia, one case of isovaleric acidemia, one case of argininemia, one case of citrullinemia I and four cases of primary carnitine deficiency were confirmed by genetic testing, which yielded an overall diagnostic rate of 5.1% (14/277). CONCLUSION: Our result has provided further evidence for the co-occurrence of ASD and IEM. Tandem mass spectrometry has a great value for the diagnosis and treatment of ASD in childhood.

T59, a New Compound Reconstructed from Curcumin, Induces Cell Apoptosis through Reactive Oxygen Species Activation in Human Lung Cancer Cells.

Curcumin is acknowledged for its antioxidant, anti-inflammatory, anti-cancer, and wound-healing properties. However, the biological activity and the molecular mechanisms of T59, which is a new derivative of curcumin, are not fully understood. The present study was aimed to determine the cytoxicity role of T59 in human lung cancer and the molecular mechanisms. Cytotoxicity and cell apoptosis effects induced by T59 were determined by MTT, AO staining, Annexin V, and JC-1. Compared with curcumin, T59 exerted more effective cytotoxicity and cell apoptosis effects in A549 and H1975. With the decreasing level of the mitochondrion membrane potential, the generation of reactive oxygen species (ROS) was increased and induced by T59. Furthermore, the expressions of cleaved-caspase-3 and Bax were increased, which were reversed by NAC mainly through the PI3K/AKT signaling pathway. Our results suggested that T59 has the potential for further investigation and study to act as an anti-cancer therapeutic against human lung cancer.

A global survey of bacterial type III secretion systems and their effectors.

The type III secretion system (T3SS) is an important genetic determinant that mediates interactions between Gram-negative bacteria and their eukaryotic hosts. Our understanding of the T3SS continues to expand, yet the availability of new bacterial genomes prompts questions about its diversity, distribution and evolution. Through a comprehensive survey of ∼20 000 bacterial genomes, we identified 174 non-redundant T3SSs from 109 genera and 5 phyla. Many of the bacteria are environmental strains that have not been reported to interact with eukaryotic hosts, while several species groups carry multiple T3SSs. Four ultra-conserved Microsynteny Blocks (MSBs) were defined within the T3SSs, facilitating comprehensive clustering of the T3SSs into 13 major categories, and establishing the largest diversity of T3SSs to date. We subsequently extended our search to identify type III effectors, resulting in 8740 candidate effectors. Lastly, an analysis of the key transcriptional regulators and circuits for the T3SS families revealed that low-level T3SS regulators were more conserved than higher-level regulators. This comprehensive analysis of the T3SSs and their protein effectors provides new insight into the diversity of systems used to facilitate host-bacterial interactions.

TRIM14 is a mitochondrial adaptor that facilitates retinoic acid-inducible gene-I-like receptor-mediated innate immune response.

Innate immunity provides the first line of host defense against invading microbial pathogens. This defense involves retinoic acid-inducible gene-I-like receptors that detect viral RNA and activate the mitochondrial antiviral-signaling (MAVS) protein, an adaptor protein, leading to activation of the innate antiviral immune response. The mechanisms by which the MAVS signalosome assembles on mitochondria are only partially understood. Here, we identify tripartite motif 14 (TRIM14) as a mediator in the immune response against viral infection. TRIM14 localizes to the outer membrane of mitochondria and interacts with MAVS. Upon viral infection, TRIM14 undergoes Lys-63-linked polyubiquitination at Lys-365 and recruits NF-κB essential modulator to the MAVS signalosome, leading to the activation of both the IFN regulatory factor 3 and NF-κB pathways. Knockdown of TRIM14 disrupts the association between NF-κB essential modulator and MAVS and attenuates the antiviral response. Our results indicate that TRIM14 is a component of the mitochondrial antiviral immunity that facilitates the immune response mediated by retinoic acid-inducible gene-I-like receptors.

Distribution and Evolution of Yersinia Leucine-Rich Repeat Proteins.

Leucine-rich repeat (LRR) proteins are widely distributed in bacteria, playing important roles in various protein-protein interaction processes. In Yersinia, the well-characterized type III secreted effector YopM also belongs to the LRR protein family and is encoded by virulence plasmids. However, little has been known about other LRR members encoded by Yersinia genomes or their evolution. In this study, the Yersinia LRR proteins were comprehensively screened, categorized, and compared. The LRR proteins encoded by chromosomes (LRR1 proteins) appeared to be more similar to each other and different from those encoded by plasmids (LRR2 proteins) with regard to repeat-unit length, amino acid composition profile, and gene expression regulation circuits. LRR1 proteins were also different from LRR2 proteins in that the LRR1 proteins contained an E3 ligase domain (NEL domain) in the C-terminal region or an NEL domain-encoding nucleotide relic in flanking genomic sequences. The LRR1 protein-encoding genes (LRR1 genes) varied dramatically and were categorized into 4 subgroups (a to d), with the LRR1a to -c genes evolving from the same ancestor and LRR1d genes evolving from another ancestor. The consensus and ancestor repeat-unit sequences were inferred for different LRR1 protein subgroups by use of a maximum parsimony modeling strategy. Structural modeling disclosed very similar repeat-unit structures between LRR1 and LRR2 proteins despite the different unit lengths and amino acid compositions. Structural constraints may serve as the driving force to explain the observed mutations in the LRR regions. This study suggests that there may be functional variation and lays the foundation for future experiments investigating the functions of the chromosomally encoded LRR proteins of Yersinia.