The atypical organization of the luxI/R family genes in AHL-driven quorum-sensing circuits.

Quorum sensing (QS) is an elaborate regulatory mechanism associated with virulence and bacterial adaptation to the changing environment. QS is widespread in Proteobacteria and acts primarily through N-acylhomoserine lactone (AHL) signals. At the core of the AHL-driven QS systems are the AHL synthase gene (luxI family) and its cognate transcriptional regulator gene (luxR family). Several QS systems display one or more genes intervening between the luxI and luxR, in which gene arrangements are notably different due to the relative position and the transcriptional orientation between the essential luxI/R and the genes of location correlation. These adjacent genes may exert a regulatory impact on the primary QS genes or contribute toward an extension of QS regulatory control. In this review, we describe the organization of AHL-driven QS genes based on previous research and specific genome databases and provide new insights into these atypical QS gene arrangements.

Soybean-mediated suppression of BjaI/BjaR1 quorum sensing in Bradyrhizobium diazoefficiens impacts symbiotic nitrogen fixation.

The acyl-homoserine lactones (AHLs)-mediated LuxI/LuxR quorum sensing (QS) system orchestrates diverse bacterial behaviors in response to changes in population density. The role of the BjaI/BjaR1 QS system in Bradyrhizobium diazoefficiens USDA 110, which shares homology with LuxI/LuxR, remains elusive during symbiotic interaction with soybean. Here this genetic system in wild-type (WT) bacteria residing inside nodules exhibited significantly reduced activity compared to free-living cells, potentially attributed to soybean-mediated suppression. The deletion mutant strain ΔbjaR1 showed significantly enhanced nodulation induction and nitrogen fixation ability. Nevertheless, its ultimate symbiotic outcome (plant dry weight) in soybeans was compromised. Furthermore, comparative analysis of the transcriptome, proteome, and promoter activity revealed that the inactivation of BjaR1 systematically activated and inhibited genomic modules associated with nodulation and nitrogen metabolism. The former appeared to be linked to a significant decrease in the expression of NodD2, a key cell-density-dependent repressor of nodulation genes, while the latter conferred bacterial growth and nitrogen fixation insensitivity to environmental nitrogen. In addition, BjaR1 exerted a positive influence on the transcription of multiple genes involved in a so-called central intermediate metabolism within the nodule. In conclusion, our findings highlight the crucial role of the BjaI/BjaR1 QS circuit in positively regulating bacterial nitrogen metabolism and emphasize the significance of the soybean-mediated suppression of this genetic system for promoting efficient symbiotic nitrogen fixation by B. diazoefficiens.IMPORTANCEThe present study demonstrates, for the first time, that the BjaI/BjaR1 QS system of Bradyrhizobium diazoefficiens has a significant impact on its nodulation and nitrogen fixation capability in soybean by positively regulating NodD2 expression and bacterial nitrogen metabolism. Moreover, it provides novel insights into the importance of suppressing the activity of this QS circuit by the soybean host plant in establishing an efficient mutual relationship between the two symbiotic partners. This research expands our understanding of legumes' role in modulating symbiotic nitrogen fixation through rhizobial QS-mediated metabolic functioning, thereby deepening our comprehension of symbiotic coevolution theory. In addition, these findings may hold great promise for developing quorum quenching technology in agriculture.

RsaM: a unique dominant regulator of AHL quorum sensing in bacteria.

Quorum sensing (QS) in proteobacteria is a mechanism to control gene expression orchestrated by the LuxI/LuxR protein family pair, which produces and responds to N-acyl homoserine lactone (AHL) diffusible signal molecules. QS is often regarded as a cell density response via the sensing of/response to the concentrations of AHLs, which are constantly basally produced by bacterial cells. The luxI/R systems, however, undergo supra-regulation in response to external stimuli and many regulators have been implicated in controlling QS in bacteria, although it remains unclear how most of these regulators and cues contribute to the QS response. One regulator, called RsaM, has been reported in a few proteobacterial species to have a stringent role in the control of AHL QS. RsaMs are small, in the range of 140-170 aa long, and are found in several genera, principally in Burkholderia and Acinetobacter. The gene encoding RsaM is always located as an independent transcriptional unit, situated adjacent to QS luxI and/or luxR loci. One of the most remarkable aspects of RsaM is its uniqueness; it does not fall into any of the known bacterial regulatory families and it possesses a distinct and novel fold that does not exhibit binding affinity for nucleic acids or AHLs. RsaM stands out as a distinctive regulator in bacteria, as it is likely to have an important ecological role, as well as unravelling a novel way of gene regulation in bacteria.

Effect of lipopeptide extracted from Bacillus licheniformis on the expression of bap and luxI genes in multi-drug-resistant Acinetobacter baumannii and Pseudomonas aeruginosa.

Recently, opportunistic pathogens like Acinetobacter baumannii and Pseudomonas aeruginosa have caused concern due to their ability to cause antibiotic resistance in weakened immune systems. As a result, researchers are always seeking efficient antimicrobial agents to tackle this issue. The hypothesis of the recent study was that probiotic products derived from bacteria would be effective in reducing drug resistance in other bacteria. This research aimed to investigate the antimicrobial properties of probiotic products from various bacterial strains, including Lactobacillus rhamnosus, Pediococcus acidilactisi, Bacillus coagulans, Bacillus subtilis, and Bacillus licheniformis. These were tested against multi-drug-resistant (MDR) standard strains A. baumannii and P. aeruginosa. B. licheniformis was found to be the most effective probiotic strain, possessing the LanA and LanM lantibiotic genes. The lipopeptide nature of the probiotic product was confirmed through high-performance liquid chromatography (HPLC) and Fourier-transform infrared spectroscopy (FTIR) techniques. The anti-biofilm and antimicrobial properties of this probiotic were measured using an SEM electron microscope and minimum inhibitory concentration (MIC) test. Real-time PCR (qPCR) was used to compare the expression of bap and luxI genes, which are considered virulence factors of drug-resistant bacteria, before and after treatment with antimicrobial agents. The MIC results showed that the probiotic product prevented the growth of bacteria at lower concentrations compared to antibiotics. In addition, the ΔΔCqs indicated that gene expression was significantly down-regulated following treatment with the obtained probiotic product. It was found that B. licheniformis probiotic products could reduce drug resistance in other bacteria, making it a potential solution to antibiotic resistance.

Characterization of differentiated autoregulation of LuxI/LuxR-type quorum sensing system in Pseudoalteromonas.

Gram-negative bacteria usually use acyl-homoserine lactones (AHLs)-mediated LuxI/LuxR-type quorum sensing (QS) systems for cell-cell cooperation and/or bacteria-environment communication. LuxI and LuxR are AHLs synthase and receptor, respectively. These two parts could form a positive regulatory feedback loop, controlling various types of group behaviors. However, the autoregulation mechanisms between them are fragmented and could be highly differentiated in different bacteria. Here, we clarified the autoregulation mechanism between LuxI and LuxR in Pseudoalteromonas sp. R3. YasI (LuxI in strain R3) synthesizes two types of AHLs, C8-HSL and 3-OH-C8-HSL. It is worth noting that YasR (LuxR in strain R3) only responds to C8-HSL rather than 3-OH-C8-HSL. YasR-C8HSL can activate the yasI transcription by recognizing "lux box" at yasI upstream. Interestingly, YasR can directly promote the yasR expression with AHL-independent manner, but AHL absence caused by the yasI-deficiency led to the significant decrease in the yasR expression. Further study demonstrated that the yasI-deficiency can result in the decrease in the yasR mRNA stability. Notably, both yasI-deficiency and yasR-deficiency led to the significant decrease in the expression of hfq encoding RNA chaperone. Therefore, it was speculated that not only YasR itself can directly regulate the yasR transcription, but YasR-C8HSL complex indirectly affects the yasR mRNA stability by regulating Hfq.

In silico analysis of AhyI protein and AI-1 inhibition using N-cis-octadec-9z-enoyl-l-homoserine lactone inhibitor in Aeromonas hydrophila.

AhyI is homologous to the protein LuxI and is conserved throughout bacterial species including Aeromonas hydrophila. A. hydrophila causes opportunistic infections in fish and other aquatic organisms. Furthermore, this pathogennot only poses a great risk for the aquaculture industry, but also for human public health. AhyI (expressing acylhomoserine lactone) is responsible for the biosynthesis of autoinducer-1 (AI-1), commonly referred to as a quorum sensing (QS) signaling molecule, which plays an essential role in bacterial communication. Studying protein structure is essential for understanding molecular mechanisms of pathogenicity in microbes. Here, we have deduced a predicted structure of AhyI protein and characterized its function using in silico methods to aid the development of new treatments for controlling A.hydrophila infections. In addition to modeling AhyI, an appropriate inhibitor molecule was identified via high throughput virtual screening (HTVS) using mcule drug-like databases.The AhyI-inhibitor N-cis-octadec-9Z-enoyl-l-Homoserine lactone was selected withthe best drug score. In order to understand the pocket sites (ligand binding sites) and their interaction with the selected inhibitor, docking (predicted protein binding complex) servers were used and the selected ligand was docked with the predicted AhyI protein model. Remarkably, N-cis-octadec-9Z-enoyl-l-Homoserine lactone established interfaces with the protein via16 residues (V24, R27, F28, R31, W34, V36, D45, M77, F82, T101, R102, L103, 104, V143, S145, and V168), which are involved with regulating mechanisms of inhibition. These proposed predictions suggest that this inhibitor molecule may be used as a novel drug candidate for the inhibition of auto-inducer-1 (AI-1) activity.The N-cis-octadec-9Z-enoyl-l-Homoserine lactone inhibitor molecule was studied on cultured bacteria to validate its potency against AI-1 production. At a concentration of 40 µM, optimal inhibition efficiency of AI-1 was observedin bacterial culture media.These results suggest that the inhibitor molecule N-cis-octadec-9Z-enoyl-l-Homoserine lactone is a competitive inhibitor of AI-1 biosynthesis.

E. coli biosensor based on modular GFP and luxI/luxR cyclic amplification circuit for sensitive detection of lysine.

In this study, an E. coli biosensor based on modular green fluorescent protein and luxI/IuxR cycle amplification circuit was constructed for sensitive detection of bioavailable lysine. The results indicated that the luxI/IuxR positive feedback circuit based on quorum sensing can be used as a signal amplifier to improve the sensitivity to lysine detection with the detection limit of 256 nM. The presented method was more sensitive than the previously reported whole-cell fluorescent microbial biosensors. In addition, the developed E. coli biosensor was specific for lysine detection, and other amino acids and proteins did not cause any interference. The constructed genetic engineered biosensor was accurate for lysine detection, the lysine content of 6.87 ± 0.36% in tryptone was successfully measured, and after adding 10, 30, and 50 µM lysine in tryptone, the recoveries of 109.98 ± 10.44%, 103.88 ± 7.66%, and 105.89 ± 6.34% were obtained, respectively. Furthermore, as the design of the genetic engineered biosensor is modular, it can conceivably be utilized as a component in the design of more complex synthetic gene circuits without any changes to the amplifier and reporter system.

Identification of candidate genes associated with slaughter traits in F2 chicken population using genome-wide association study.

Slaughter traits are crucial economic traits of chickens. We performed a GWAS to discover critical loci and candidate genes for 21 slaughter traits in an F2 chicken population resulting from crossing Luxi gamecocks and recessive white feather broilers. We found some SNPs and genes which were significantly associated with keel length, head length, body slope length, bilateral leg weight without shin, bilateral foot weight, subcutaneous fat thickness, heart weight, muscular stomach weight and glandular stomach weight. This study provides references for further investigation of slaughter traits and molecular breeding in chicken.

A novel 23 bp indel mutation in PRL gene is associated with growth traits in Luxi Blackhead sheep.

Prolactin is a highly versatile pituitary hormone with multiple biological functions. PRL expression is regulated by POU1F1 and the prophet of POU1F1 (PROP1). The aim of this study was to investigate the indel variations in ovine PRL and the directly related (PROP1 and POU1F1) genes, and their associations with growth traits in Luxi Blackhead (LXBH) sheep. A monomorphism in PROP1 and POU1F1 genes, and one novel 23-bp insertion mutation in the PRL gene, were identified in LXBH sheep. The 23 bp insertion mutation within PRL gene was significantly associated with several body measurements (e.g., body weight, body height) in sheep of different ages (p < 0.05). Ram lambs (p = 0.036) of genotype insertion/insertion (II) had significantly higher body weights. Weaners (p = 0.018) of genotypes insertion/insertion (II) and insertion/deletion (ID) also had significantly higher body weights compared with male sheep of deletion/deletion (DD) genotype. Moreover, among ewe lambs, individuals of genotype insertion/insertion (II) had a higher paunch girth compared to those with other genotypes (p = 0.044). These findings indicate that a 23 bp indel variant of the ovine PRL gene is correlated with body measurements in LXBH sheep. The findings have potential utility for sheep breeding programs based on marker-assisted selection.

Quorum sensing communication: Bradyrhizobium-Azospirillum interaction via N-acyl-homoserine lactones in the promotion of soybean symbiosis.

Quorum-sensing (QS) mechanisms are important in intra- and inter-specific communication among bacteria. We investigated QS mechanisms in Bradyrhizobium japonicum strain CPAC 15 and Azospirillum brasilense strains Ab-V5 and Ab-V6, used in commercial co-inoculants for the soybean crop in Brazil. A transconjugant of CPAC 15-QS with partial inactivation of N-acyl-homoserine lactones (AHLs) was obtained and several parameters were evaluated; in vitro, CPAC 15 and the transconjugant differed in growth, but not in biofilm formation, and no differences were observed in the symbiotic performance in vivo. The genome of CPAC 15 carries functional luxI and luxR genes and low amounts of three AHL molecules were detected: 3-OH-C12-AHL, 3-OH-C14-AHL, and 3-oxo-C14-AHL. Multiple copies of luxR-like genes, but not of luxI are present in the genomes of Ab-V5 and Ab-V6, and differences in gene expression were observed when the strains were co-cultured with B. japonicum; we may infer that the luxR-genes of A. brasilense may perceive the AHL molecules of B. japonicum. Soybean symbiotic performance was improved especially by co-inoculation with Ab-V6, which, contrarily to Ab-V5, did not respond to the AHLs of CPAC 15. We concluded that A. brasilense Ab-V5, but not Ab-V6, responded to the QS signals of CPAC 15, and that the synergistic interaction may be credited, at least partially, to the QS interaction. In addition, we confirmed inter- and intra-species QS communication between B. japonicum and A. brasilense and, for Azospirillum, at the strain level, impacting several steps of the symbiosis, from cell growth to plant nodulation and growth.

Autonomous control of metabolic state by a quorum sensing (QS)-mediated regulator for bisabolene production in engineered E. coli.

Inducible gene expression systems are widely used in microbial host strains for protein and commodity chemical production because of their extensive characterization and ease of use. However, some of these systems have disadvantages such as leaky expression, lack of dynamic control, and the prohibitively high costs of inducers associated with large-scale production. Quorum sensing (QS) systems in bacteria control gene expression in response to population density, and the LuxI/R system from Vibrio fischeri is a well-studied example. A QS system could be ideal for biofuel production strains as it is self-regulated and does not require the addition of inducer compounds, which reduce operational costs for inducer. In this study, a QS system was developed for inducer-free production of the biofuel compound bisabolene from engineered E. coli. Seven variants of the Sensor plasmid, which carry the luxI-luxR genes, and four variants of the Response plasmid, which carry bisabolene producing pathway genes under the control of the PluxI promoter, were designed for optimization of bisabolene production. Furthermore, a chromosome-integrated QS strain was engineered with the best combination of Sensor and Response plasmid and produced bisabolene at a titer of 1.1g/L without addition of external inducers. This is a 44% improvement from our previous inducible system. The QS strain also displayed higher homogeneity in gene expression and isoprenoid production compared to an inducible-system strain.

Characterization of two LuxI/R homologs in Pantoea ananatis LMG 2665T.

Quorum sensing (QS) plays an important role in the regulation of bacteria-host interactions and ecological fitness in many bacteria. In this study, 2 luxI/R homologs, namely eanI/eanR and rhlI/rhlR, were identified in the genome sequence of Pantoea ananatis LMG 2665T. To determine a role for these luxI/R homologs in pathogenicity and biofilm formation, mutant bacterial strains lacking either eanI/R or rhlI/R and both of these homologs were generated. The results indicated that both the RhlI/R and EanI/R systems are required for pathogenicity and biofilm formation in strain LMG 2665T. This is the first study to characterize the biological significance of the RhlI/R QS system in P. ananatis.

Traveling waves in response to a diffusing quorum sensing signal in spatially-extended bacterial colonies.

In the behavior known as quorum sensing (QS), bacteria release diffusible signal molecules known as autoinducers, which by accumulating in the environment induce population-wide changes in gene expression. Although QS has been extensively studied in well-mixed systems, the ability of diffusing QS signals to synchronize gene expression in spatially extended colonies is not well understood. Here we investigate the one-dimensional spatial propagation of QS-circuit activation in a simple, analytically tractable reaction-diffusion model for the LuxR-LuxI circuit, which regulates bioluminescence of the marine bacterium Aliivibrio fischeri. The quorum activation loop is modeled by a Hill function with a cooperativity exponent (m=2.2). The model is parameterized from laboratory data and captures the major empirical properties of the LuxR-LuxI system and its QS regulation of A. fischeri bioluminescence. Our simulations of the model show propagating waves of activation or deactivation of the QS circuit in a spatially extended colony. We further prove analytically that the model equations possess a traveling wave solution. This mathematical proof yields the rate of autoinducer degradation that is compatible with a traveling wave of gene expression as well as the critical degradation rate at which the nature of the wave switches from activation to deactivation. Our results can be used to predict the direction and activating or deactivating nature of a wave of gene expression in experimentally controlled bacterial populations subject to a diffusing autoinducer signal.

Identification of genomic diversity and selection signatures in Luxi cattle using whole-genome sequencing data.

OBJECTIVE: The objective of this study was to investigate the genetic diversity, population structure and whole-genome selection signatures of Luxi cattle to reveal its genomic characteristics in terms of meat and carcass traits, skeletal muscle development, body size, and other traits. METHODS: To further analyze the genomic characteristics of Luxi cattle, this study sequenced the whole-genome of 16 individuals from the core conservation farm in Shandong region, and collected 174 published genomes of cattle for conjoint analysis. Furthermore, three different statistics (pi, Fst, and XP-EHH) were used to detect potential positive selection signatures related to selection in Luxi cattle. Moreover, gene ontology and Kyoto encyclopedia of genes and genomes pathway enrichment analyses were performed to reveal the potential biological function of candidate genes harbored in selected regions. RESULTS: The results showed that Luxi cattle had high genomic diversity and low inbreeding levels. Using three complementary methods (pi, Fst, and XP-EHH) to detect the signatures of selection in the Luxi cattle genome, there were 2,941, 2,221 and 1,304 potentially selected genes identified, respectively. Furthermore, there were 45 genes annotated in common overlapping genomic regions covered 0.723 Mb, including PLAG1 zinc finger (PLAG1), dedicator of cytokinesis 3 (DOCK3), ephrin A2 (EFNA2), DAZ associated protein 1 (DAZAP1), Ral GTPase activating protein catalytic subunit alpha 1 (RALGAPA1), mediator complex subunit 13 (MED13), and decaprenyl diphosphate synthase subunit 2 (PDSS2), most of which were enriched in pathways related to muscle growth and differentiation and immunity. CONCLUSION: In this study, we provided a series of genes associated with important economic traits were found in positive selection regions, and a scientific basis for the scientific conservation and genetic improvement of Luxi cattle.

Development of a Quorum Sensing-Mediated Bacterial Autolytic System in Escherichia coli for Automatic Release of Intracellular Products.

Escherichia coli, one of the most efficient expression hosts for recombinant proteins, is widely used in chemical, medical, food, and other industries. De novo engineering of gene regulation circuits and cell density-controlled E. coli cell lysis are promising directions for the release of intracellular bioproducts. Here, we developed an E. coli autolytic system, named the quorum sensing-mediated bacterial autolytic (QS-BA) system, by incorporating an acyl-homoserine lactone (AHL)-based YasI/YasR-type quorum sensing circuit from Pseudoalteromonas into E. coli cells. The results showed that the E. coli QS-BA system can release the intracellular bioproducts into the cell culture medium in terms of E. coli cell density, which offers an environmentally-friendly, economical, efficient, and flexible E. coli lysis platform for production of recombinant proteins. The QS-BA system has the potential to serve as an integrated system for the large-scale production of target products in E. coli for medical and industrial applications.

Regulation of quorum sensing activities by the stringent response gene rsh in sphingomonads is species-specific and culture condition dependent.

Stringent response and quorum sensing (QS) are two essential mechanisms that control bacterial global metabolism for better survival. Sphingomonads are a clade of bacteria that survive successfully in diverse ecosystems. In silico survey indicated that 36 out of 79 investigated sphingomonads strains contained more than one luxI homolog, the gene responsible for the biosynthesis of QS signal acyl homoserine lactones (AHLs). Investigation of the regulatory effects of the stringent response gene rsh on QS related bioactivities were carried out using rsh mutants of Sphingobium japonicum UT26 and Sphingobium sp. SYK-6, both had three luxI homologs. Results indicated that deletion of rsh upregulated the overall production of AHLs and extracellular polymeric substances (EPS) in both UT26 and SYK-6 in rich medium, but affected expressions of these luxI/luxR homologs in different ways. In the poor medium (1% LB), rsh mutant of SYK-6 significantly lost AHLs production in broth cultivation but not in biofilm cultivation. The regulatory effects of rsh on QS activities were growth phase dependent in UT26 and culture condition dependent in SYK-6. Our results demonstrated the negative regulatory effect of rsh on QS activities in sphingomonads, which were very different from the positive effect found in sphingomonads containing only one luxI/R circuit. This study extends the current knowledge on the intricate networks between stringent response and QS system in sphingomonads, which would help to understand their survival advantage.

A Mesorhizobium japonicum quorum sensing circuit that involves three linked genes and an unusual acyl-homoserine lactone signal.

Members of the genus Mesorhizobium, which are core components of the rhizosphere and specific symbionts of legume plants, possess genes for acyl-homoserine lactone (AHL) quorum sensing (QS). Here we show Mesorhizobium japonicum MAFF 303099 (formerly M. loti) synthesizes and responds to N-[(2E, 4E)-2,4-dodecadienoyl] homoserine lactone (2E, 4E-C12:2-HSL). We show that the 2E, 4E-C12:2-HSL QS circuit involves one of four luxR-luxI-type genes found in the sequenced genome of MAFF 303099. We refer to this circuit, which appears to be conserved among Mesorhizobium species, as R1-I1. We show that two other Mesorhizobium strains also produce 2E, 4E-C12:2-HSL. The 2E, 4E-C12:2-HSL is unique among known AHLs in its arrangement of two trans double bonds. The R1 response to 2E, 4E-C12:2-HSL is extremely selective in comparison with other LuxR homologs, and the trans double bonds appear critical for R1 signal recognition. Most well-studied LuxI-like proteins use S-adenosylmethionine and an acyl-acyl carrier protein as substrates for synthesis of AHLs. Others that form a subgroup of LuxI-type proteins use acyl-coenzyme A substrates rather than acyl-acyl carrier proteins. I1 clusters with the acyl-coenzyme A-type AHL synthases. We show that a gene linked to the I1 AHL synthase is involved in the production of the QS signal. The discovery of the unique I1 product enforces the view that further study of acyl-coenzyme A-dependent LuxI homologs will expand our knowledge of AHL diversity. The involvement of an additional enzyme in AHL generation leads us to consider this system a three-component QS circuit. IMPORTANCE We report a Mesorhizobium japonicum quorum sensing (QS) system involving a novel acyl-homoserine lactone (AHL) signal. This system is known to be involved in root nodule symbiosis with host plants. The chemistry of the newly described QS signal indicated that there may be a dedicated cellular enzyme involved in its synthesis in addition to the types known for production of other AHLs. Indeed, we report that an additional gene is required for synthesis of the unique signal, and we propose that this is a three-component QS circuit as opposed to the canonical two-component AHL QS circuits. The signaling system is exquisitely selective. The selectivity may be important when this species resides in the complex microbial communities around host plants and may make this system useful in various synthetic biology applications of QS circuits.

Genome-Wide Identification and Characterization of Long Non-Coding RNAs in Longissimus dorsi Skeletal Muscle of Shandong Black Cattle and Luxi Cattle.

There is an increasing understanding of the possible regulatory role of long non-coding RNAs (LncRNA). Studies on livestock have mainly focused on the regulation of cell differentiation, fat synthesis, and embryonic development. However, there has been little study of skeletal muscle of domestic animals and the potential role of lncRNA. In this study, the transcriptome numbers of longissimus muscle of different beef cattle (Shandong black catle and Luxi catlle) were used to construct muscle related lncRNAs-miRNA-mRNA interaction network through bioinformatics analysis. This is helpful to clarify the molecular mechanism of bovine muscle development, and can be used to promote animal husbandry and improve animal husbandry production. According to the screening criteria of |FC|≧2 and q < 0.05, a total of 1,415 transcripts (of which 480 were LncRNAs) were differentially expressed (q < 0.05) in the different breeds. Further, we found that the most differentially expressed LncRNAs were found on chromosome 9, in which the differentially expressed LncRNAs targeted 1,164 protein coding genes (MYORG, Wnt4, PAK1, ADCY7,etc) (upstream and downstream<50 Kb). In addition, Pearson's correlation coefficients of co-expression levels indicated a potential trans regulatory relationship between the differentially expressed LncRNAs and 43844 mRNAs (r > 0.9). The identified co-expressed mRNAs (MYORG, Dll1, EFNB2, SOX6, MYOCD, and MYLK3) are related to the formation of muscle structure, and enriched in muscle system process, strained muscle cell differentiation, muscle cell development, striated muscle tissue development, calcium signaling, and AMPK signaling. Additionally, we also found that some LncRNAs (LOC112444238, LOC101903367, LOC104975788, LOC112441863, LOC112449549, and LOC101907194) may interact with miRNAs related to cattle muscle growth and development. Based on this, we constructed a LncRNAs-miRNA-mRNA interaction network as the putative basis for biological regulation in cattle skeletal muscle. Interestingly, a candidate differential LncRNA (LOC104975788) and a protein-coding gene (Pax7) contain miR-133a binding sites and binding was confirmed by luciferase reporter assay. LOC104975788 may combined miR-133a competitively with Pax7, thus relieving the inhibitory effect of miR-133a on Pax7 to regulate skeletal muscle development. These results will provide the theoretical basis for further study of LncRNA regulation and activity in different cattle breeds.

Whole genome sequencing of Luxi Black Head sheep for screening selection signatures associated with important traits.

OBJECTIVE: Luxi Black Head sheep (LBH) is the first crossbreed specialized for meat production and was developed by crossbreeding Black Head Dorper sheep (DP) and Small Tailed Han sheep (STH) in the farming areas of northern China. Research on the genomic variations and selection signatures of LBH caused by continuous artificial selection is of great significance for identifying the genetic mechanisms of important traits of sheep and for the continuous breeding of LBH. METHODS: We explored the genetic relationships of LBH, DP, and several Mongolian sheep breeds by constructing phylogenetic tree, principal component analysis and linkage disequilibrium analysis. In addition, we analysed 29 whole genomes of sheep. The genomewide selection signatures have been scanned with four methods heterozygosity (HP), fixation index (FST), cross-population extended haplotype homozygosity (XP-EHH) and the nucleotide diversity (θπ) ratio. RESULTS: The genetic relationships analysis showed that LBH appeared to be an independent cluster closer to DP. The candidate signatures of positive selection in sheep genome revealed candidate genes for developmental process (HoxA gene cluster, BCL2L11, TSHR), immunity (CXCL6, CXCL1, SKAP2, PTK6, MST1R), growth (PDGFD, FGF18, SRF, SOCS2), and reproduction (BCAS3, TRIM24, ASTL, FNDC3A). Moreover, two signalling pathways closely related to reproduction, the thyroid hormone signalling pathway and the oxytocin signalling pathway, were detected. CONCLUSION: The selective sweep analysis of LBH genome revealed candidate genes and signalling pathways associated with developmental process, immunity, growth, and reproduction. Our findings provide a valuable resource for sheep breeding and insight into the mechanisms of artificial selection.

Identification of small molecules that strongly inhibit bacterial quorum sensing using a high-throughput lipid vesicle lysis assay.

Strategies to both monitor and block bacterial quorum sensing (QS), and thus associated infections, are of significant interest. We developed a straightforward assay to monitor biosurfactants and lytic agents produced by bacteria under the control of QS. The method is based on the lysis of synthetic lipid vesicles containing the environmentally sensitive fluorescent dye calcein. This assay allows for the in situ screening of compounds capable of altering biosurfactant production by bacteria, and thereby the identification of molecules that could potentially modulate QS pathways, and avoids the constraints of many of the cell-based assays in use today. Application of this assay in a high-throughput format revealed five molecules capable of blocking vesicle lysis by S. aureus. Two of these compounds were found to almost completely inhibit agr-based QS in S. aureus and represent the most potent small-molecule-derived QS inhibitors reported in this formidable pathogen.