Comparative Genomics And Functional Analysis Of Rhamnose Catabolic Pathways And Regulons In Bacteria

L-rhamnose (Rha) is a deoxy-hexose sugar commonly found in nature. L-Rha catabolic pathways were previously characterized in various bacteria including Escherichia coli. Nevertheless, homology searches failed to recognize all the genes for the complete L Rha utilization pathways in diverse microbial species involved in biomass decomposition. Moreover, the regulatory mechanisms of L-Rha catabolism have remained unclear in most species. A comparative genomics approach was used to reconstruct the L-Rha catabolic pathways and transcriptional regulons in the phyla Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria, and Thermotogae. The reconstructed pathways include multiple novel enzymes and transporters involved in the utilization of L-Rha and L-Rha-containing polymers. Large-scale regulon inference using bioinformatics revealed remarkable variations in transcriptional regulators for L-Rha utilization genes among bacteria. A novel bifunctional enzyme, L-rhamnulose-phosphate aldolase (RhaE) fused to L-lactaldehyde dehydrogenase (RhaW), which is not homologous to previously characterized L-Rha catabolic enzymes, was identified in diverse bacteria including Chloroflexi, Bacilli, and Alphaproteobacteria. By using in vitro biochemical assays we validated both enzymatic activities of the purified recombinant RhaEW proteins from Chloroflexus aurantiacus and Bacillus subtilis. Another novel enzyme of the L-Rha catabolism, L-lactaldehyde reductase (RhaZ), was identified in Gammaproteobacteria and experimentally validated by in vitro enzymatic assays using the recombinant protein from Salmonella typhimurium. C. aurantiacus induced transcription of the predicted L-Rha utilization genes when L-Rha was present in the growth medium and consumed L-Rha from the medium. This study provided comprehensive insights to L-Rha catabolism and its regulation in diverse Bacteria

Hallmarks of the Mott-Metal Crossover in the Hole-Doped Pseudospin-1/2 Mott Insulator Sr\u3csub\u3e2\u3c/sub\u3eIrO\u3csub\u3e4\u3c/sub\u3e

The physics of doped Mott insulators remains controversial after decades of active research, hindered by the interplay among competing orders and fluctuations. It is thus highly desired to distinguish the intrinsic characters of the Mott-metal crossover from those of other origins. Here we investigate the evolution of electronic structure and dynamics of the hole-doped pseudospin-1/2 Mott insulator Sr2IrO4. The effective hole doping is achieved by replacing Ir with Rh atoms, with the chemical potential immediately jumping to or near the top of the lower Hubbard band. The doped iridates exhibit multiple iconic low-energy features previously observed in doped cuprates—pseudogaps, Fermi arcs and marginal-Fermi-liquid-like electronic scattering rates. We suggest these signatures are most likely an integral part of the material’s proximity to the Mott state, rather than from many of the most claimed mechanisms, including preformed electron pairing, quantum criticality or density-wave formation

Genotyping by sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding

Marker-assisted selection (MAS) refers to the use of molecular markers to assist phenotypic selections in crop improvement. Several types of molecular markers, such as single nucleotide polymorphism (SNP), have been identified and effectively used in plant breeding. The application of next-generation sequencing (NGS) technologies has led to remarkable advances in whole genome sequencing, which provides ultra-throughput sequences to revolutionize plant genotyping and breeding. To further broaden NGS usages to large crop genomes such as maize and wheat, genotyping by sequencing (GBS) has been developed and applied in sequencing multiplexed samples that combine molecular marker discovery and genotyping. GBS is a novel application of NGS protocols for discovering and genotyping SNPs in crop genomes and populations. The GBS approach includes the digestion of genomic DNA with restriction enzymes followed by the ligation of barcode adapter, PCR amplification and sequencing of the amplified DNA pool on a single lane of flow cells. Bioinformatic pipelines are needed to analyze and interpret GBS datasets. As an ultimate MAS tool and a cost-effective technique, GBS has been successfully used in implementing genome-wide association study (GWAS), genomic diversity study, genetic linkage analysis, molecular marker discovery and genomic selection (GS) under a large scale of plant breeding programs

Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima

Hyperthermophilic bacteria from the Thermotogales lineage can produce hydrogen by fermenting a wide range of carbohydrates. Previous experimental studies identified a large fraction of genes committed to carbohydrate degradation and utilization in the model bacterium Thermotoga maritima. Knowledge of these genes enabled comprehensive reconstruction of biochemical pathways comprising the carbohydrate utilization network. However, transcriptional factors (TFs) and regulatory mechanisms driving this network remained largely unknown. Here, we used an integrated approach based on comparative analysis of genomic and transcriptomic data for the reconstruction of the carbohydrate utilization regulatory networks in 11 Thermotogales genomes. We identified DNA-binding motifs and regulons for 19 orthologous TFs in the Thermotogales. The inferred regulatory network in T. maritima contains 181 genes encoding TFs, sugar catabolic enzymes and ABC-family transporters. In contrast to many previously described bacteria, a transcriptional regulation strategy of Thermotoga does not employ global regulatory factors. The reconstructed regulatory network in T. maritima was validated by gene expression profiling on a panel of mono- and disaccharides and by in vitro DNA-binding assays. The observed upregulation of genes involved in catabolism of pectin, trehalose, cellobiose, arabinose, rhamnose, xylose, glucose, galactose, and ribose showed a strong correlation with the UxaR, TreR, BglR, CelR, AraR, RhaR, XylR, GluR, GalR, and RbsR regulons. Ultimately, this study elucidated the transcriptional regulatory network and mechanisms controlling expression of carbohydrate utilization genes in T. maritima. In addition to improving the functional annotations of associated transporters and catabolic enzymes, this research provides novel insights into the evolution of regulatory networks in Thermotogales

Hallmarks of the Mott-metal crossover in the hole-doped pseudospin-1/2 Mott insulator Sr2IrO4.

The physics of doped Mott insulators remains controversial after decades of active research, hindered by the interplay among competing orders and fluctuations. It is thus highly desired to distinguish the intrinsic characters of the Mott-metal crossover from those of other origins. Here we investigate the evolution of electronic structure and dynamics of the hole-doped pseudospin-1/2 Mott insulator Sr2IrO4. The effective hole doping is achieved by replacing Ir with Rh atoms, with the chemical potential immediately jumping to or near the top of the lower Hubbard band. The doped iridates exhibit multiple iconic low-energy features previously observed in doped cuprates-pseudogaps, Fermi arcs and marginal-Fermi-liquid-like electronic scattering rates. We suggest these signatures are most likely an integral part of the material's proximity to the Mott state, rather than from many of the most claimed mechanisms, including preformed electron pairing, quantum criticality or density-wave formation

Hallmarks of the Mott-metal crossover in the hole-doped pseudospin-1/2 Mott insulator Sr2IrO4.

The physics of doped Mott insulators remains controversial after decades of active research, hindered by the interplay among competing orders and fluctuations. It is thus highly desired to distinguish the intrinsic characters of the Mott-metal crossover from those of other origins. Here we investigate the evolution of electronic structure and dynamics of the hole-doped pseudospin-1/2 Mott insulator Sr2IrO4. The effective hole doping is achieved by replacing Ir with Rh atoms, with the chemical potential immediately jumping to or near the top of the lower Hubbard band. The doped iridates exhibit multiple iconic low-energy features previously observed in doped cuprates-pseudogaps, Fermi arcs and marginal-Fermi-liquid-like electronic scattering rates. We suggest these signatures are most likely an integral part of the material's proximity to the Mott state, rather than from many of the most claimed mechanisms, including preformed electron pairing, quantum criticality or density-wave formation