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July 7, 2019

Genome resequencing and analysis of d-lactic acid fermentation ability of Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293

Genome resequencing of D-lactic acid-producing Leuconostoc mesenteroides ATCC 8293 revealed 28 base errors in the version published in the 2017. Based on the revised genome annotation, four genes encoding putative D- lactate dehydrogenases were identified. The transcriptional expression of each gene was analyzed at different growth phases and the functionality of each gene was studied in Escherichia coli. Bioreactor studies indicated that L. mesenteroides ATCC 8293 produced D-lactic acid and ethanol at a ratio of 1.7:1 (g/g) regardless of the glucose concentration.


July 7, 2019

Genome sequence of Halomonas hydrothermalis Y2, an efficient ectoine-producer isolated from pulp mill wastewater.

Halophilic microorganisms have great potentials towards biotechnological applications. Halomonas hydrothermalis Y2 is a halotolerant and alkaliphilic strain that isolated from the Na+-rich pulp mill wastewater. The strain is dominant in the bacterial community of pulp mill wastewater and exhibits metabolic diversity in utilizing various substrates. Here we present the genome sequence of this strain, which comprises a circular chromosome 3,933,432 bp in size and a GC content of 60.2%. Diverse genes that encoding proteins for compatible solutes synthesis and transport were identified from the genome. With a complete pathway for ectoine synthesis, the strain could produce ectoine from monosodium glutamate and further partially secreted into the medium. In addition, around 20% ectoine was increased by deleting the ectoine hydroxylase (EctD). The genome sequence we report here will provide genetic information regarding adaptive mechanisms of strain Y2 to its harsh habitat, as well as facilitate exploration of metabolic strategies for diverse compatible solutes, e.g., ectoine production. Copyright © 2018 Elsevier B.V. All rights reserved.


July 7, 2019

Complete genome sequence of soil actinobacteria Streptomyces cavourensis TJ430.

A new actinobacteria Streptomyces cavourensis TJ430 was isolated from the mountain soil collected from the southwest of China. In previous study, TJ430 showed striking bactericidal activities and strong ability of antibiotic production. Here, we report complete genome of this bacterium, consisting of 7.6?Mb linear chromosome and 0.2?Mb plasmids. It was predicted 6450 genes in chromosome and 225 genes in plasmids, as well as 12 gene islands in chromosome. Abundant genes have predicted functions in antibiotic metabolism and stress resistance. A whole-genome comparison of S. cavourensis TJ430, S. coelicolor A3(2), and S. lividans 66 indicates that TJ430 has a relatively high degree of strain specificity. The 16S rRNA phylogenetic tree shows the high identities (99.79%) of TJ430 with S. cavourensis DSM40300. TJ430 is a new and rare Streptomyces species, and analysis of its genome helps us to better understand primary metabolism mechanism of this isolate, as well as the evolutionary biology.© 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


July 7, 2019

Pathogenesis of Helicobacter pylori infection

In this review, we highlight progress in the last year in characterizing known virulence factors like flagella and the Cag type IV secretion system with sophisticated struc- tural and biochemical approaches to yield new insight on the assembly and functions of these critical virulence determinants. Several aspects of Helicobacter pylori physi- ology were newly explored this year and evaluated for their functions during stom- ach colonization, including a fascinating role for the essential protease HtrA in allowing access of H. pylori to the basolateral side of the gastric epithelium through cleavage of the tight junction protein E- cadherin to facilitate CagA delivery. Molecular biology tools standard in model bacteria, including regulated gene expression during animal infection and fluorescent reporter gene fusions, were newly applied to H. py- lori to explore functions for urease beyond initial colonization and establish high salt consumption as a mediator of gene expression changes. New sequencing technolo- gies enabled validation of long postulated roles for DNA methylation in regulating H. pylori gene expression. On the cell biology side, elegant work using lineage tracing in the murine model and organoid primary cell culture systems has provided new in- sights into how H. pylori manipulates gastric tissue functions, locally and at a dis- tance, to promote its survival in the stomach and induce pathologic changes. Finally, new work has bolstered the case for genomic variation as an important mechanism to generate phenotypic diversity during changing environmental conditions in the context of diet manipulation in animal infection models and during human experi- mental infection after vaccination.


July 7, 2019

Evolutionary emergence of drug resistance in Candida opportunistic pathogens.

Fungal infections, such as candidiasis caused by Candida, pose a problem of growing medical concern. In developed countries, the incidence of Candida infections is increasing due to the higher survival of susceptible populations, such as immunocompromised patients or the elderly. Existing treatment options are limited to few antifungal drug families with efficacies that vary depending on the infecting species. In this context, the emergence and spread of resistant Candida isolates are being increasingly reported. Understanding how resistance can evolve within naturally susceptible species is key to developing novel, more effective treatment strategies. However, in contrast to the situation of antibiotic resistance in bacteria, few studies have focused on the evolutionary mechanisms leading to drug resistance in fungal species. In this review, we will survey and discuss current knowledge on the genetic bases of resistance to antifungal drugs in Candida opportunistic pathogens. We will do so from an evolutionary genomics perspective, focusing on the possible evolutionary paths that may lead to the emergence and selection of the resistant phenotype. Finally, we will discuss the potential of future studies enabled by current developments in sequencing technologies, in vitro evolution approaches, and the analysis of serial clinical isolates.


July 7, 2019

Traditional Norwegian kveik are a genetically distinct group of domesticated Saccharomyces cerevisiae brewing yeasts.

The widespread production of fermented food and beverages has resulted in the domestication of Saccharomyces cerevisiae yeasts specifically adapted to beer production. While there is evidence beer yeast domestication was accelerated by industrialization of beer, there also exists a farmhouse brewing culture in western Norway which has passed down yeasts referred to as kveik for generations. This practice has resulted in ale yeasts which are typically highly flocculant, phenolic off flavor negative (POF-), and exhibit a high rate of fermentation, similar to previously characterized lineages of domesticated yeast. Additionally, kveik yeasts are reportedly high-temperature tolerant, likely due to the traditional practice of pitching yeast into warm (>28°C) wort. Here, we characterize kveik yeasts from 9 different Norwegian sources via PCR fingerprinting, whole genome sequencing of selected strains, phenotypic screens, and lab-scale fermentations. Phylogenetic analysis suggests that kveik yeasts form a distinct group among beer yeasts. Additionally, we identify a novel POF- loss-of-function mutation, as well as SNPs and CNVs potentially relevant to the thermotolerance, high ethanol tolerance, and high fermentation rate phenotypes of kveik strains. We also identify domestication markers related to flocculation in kveik. Taken together, the results suggest that Norwegian kveik yeasts are a genetically distinct group of domesticated beer yeasts with properties highly relevant to the brewing sector.


July 7, 2019

Genomics, GPCRs and new targets for the control of insect pests and vectors.

The pressing need for new pest control products with novel modes of action has spawned interest in small molecules and peptides targeting arthropod GPCRs. Genome sequence data and tools for reverse genetics have enabled the prediction and characterization of GPCRs from many invertebrates. We review recent work to identify, characterize and de-orphanize arthropod GPCRs, with a focus on studies that reveal exciting new functional roles for these receptors, including the regulation of metabolic resistance. We explore the potential for insecticides targeting Class A biogenic amine-binding and peptide-binding receptors, and consider the innovation required to generate pest-selective leads for development, within the context of new PCR-targeting products to control arthropod vectors of disease.Copyright © 2018. Published by Elsevier Inc.


July 7, 2019

Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations

Motivation A long-standing limitation in comparative genomic studies is the dependency on a reference genome, which hinders the spectrum of genetic diversity that can be identified across a population of organisms. This is especially true in the microbial world where genome architectures can significantly vary. There is therefore a need for computational methods that can simultaneously analyze the architectures of multiple genomes without introducing bias from a reference. Results In this article, we present Ptolemy: a novel method for studying the diversity of genome architectures—such as structural variation and pan-genomes—across a collection of microbial assemblies without the need of a reference. Ptolemy is a ‘top-down’ approach to compare whole genome assemblies. Genomes are represented as labeled multi-directed graphs—known as quivers—which are then merged into a single, canonical quiver by identifying ‘gene anchors’ via synteny analysis. The canonical quiver represents an approximate, structural alignment of all genomes in a given collection encoding structural variation across (sub-) populations within the collection. We highlight various applications of Ptolemy by analyzing structural variation and the pan-genomes of different datasets composing of Mycobacterium, Saccharomyces, Escherichia and Shigella species. Our results show that Ptolemy is flexible and can handle both conserved and highly dynamic genome architectures. Ptolemy is user-friendly—requires only FASTA-formatted assembly along with a corresponding GFF-formatted file—and resource-friendly—can align 24 genomes in ~10 mins with four CPUs and <2 GB of RAM.


July 7, 2019

DNA sequences and predicted protein structures of prot6E and sefA genes for Salmonella ser. Enteritidis detection

Genes prot6E and sefA are used as targets for detection of Salmonella enterica subsp. enterica serovar Enteritidis (Salmonella ser. Enteritidis). We investigated variations in these genes across 64 different Salmonella ser. Enteritidis strains isolated from egg and chicken samples, then used Whole Genome Sequence (WGS) data to model the structures of their protein products. Isolates were sequenced using Illumina technologies. Based on the resulting phylogenetic tree, our isolates clustered in 2 distinct clades. All isolates carried prot6E and sefA. Comparative genomic analyses indicated two non-synonymous mutations (Glycine ? Serine and Valine ? Isoleucine) of prot6E in 11 isolates (9 egg samples, 2 chicken samples). However, SWISS-MODEL was unable to clearly model the protein structure of these two mutations. We identified one non-synonymous mutation (Valine ? Glutamic Acid) in the sefA gene in 4 isolates from egg samples. The model for the protein structure of this mutant gene was clearly different from that of the other isolates studied herein. Circular maps of plasmid genomes from two PacBio platform-sequenced Salmonella ser. Enteritidis isolates revealed prot6E gene was located on the tail of the plasmid. Based on the biosynthesis of amino acids – Reference pathway in the KEGG pathway Database, the transition of amino acid from sefA Var. was a transversion from essential amino acid to non-essential amino acid, while that of prot6E Var.1 happened between the conditionally non-essential amino acid, and prot6E Var. 2 occurred between essential amino acids. Properties of these mutated amino acids, such as side-chain polarity or charge, may contribute to the occurrence and rate of mutations in prot6E and sefA. These insights can be used to improve detection methods for Salmonella ser. Enteritidis.


July 7, 2019

Omics in weed science: A perspective from genomics, transcriptomics, and metabolomics approaches

Modern high-throughput molecular and analytical tools offer exciting opportunities to gain a mechanistic understanding of unique traits of weeds. During the past decade, tremendous progress has been made within the weed science discipline using genomic techniques to gain deeper insights into weedy traits such as invasiveness, hybridization, and herbicide resistance. Though the adoption of newer “omics” techniques such as proteomics, metabolomics, and physionomics has been slow, applications of these omics platforms to study plants, especially agriculturally important crops and weeds, have been increasing over the years. In weed science, these platforms are now used more frequently to understand mechanisms of herbicide resistance, weed resistance evolution, and crop–weed interactions. Use of these techniques could help weed scientists to further reduce the knowledge gaps in understanding weedy traits. Although these techniques can provide robust insights about the molecular functioning of plants, employing a single omics platform can rarely elucidate the gene-level regulation and the associated real-time expression of weedy traits due to the complex and overlapping nature of biological interactions. Therefore, it is desirable to integrate the different omics technologies to give a better understanding of molecular functioning of biological systems. This multidimensional integrated approach can therefore offer new avenues for better understanding of questions of interest to weed scientists. This review offers a retrospective and prospective examination of omics platforms employed to investigate weed physiology and novel approaches and new technologies that can provide holistic and knowledge-based weed management strategies for future.


July 7, 2019

Complete genome sequence of an efficient vitamin D3-hydroxylating bacterium, Pseudonocardia autotrophica NBRC 12743.

Pseudonocardia autotrophica NBRC 12743 contains a cytochrome P450 vitamin D3hydroxylase, and it is used as a biocatalyst for the commercial produc- tion of hydroxyvitamin D3, a valuable compound for medication. Here, we report the complete genome sequence of P. autotrophica NBRC 12743, which could be useful for improving the productivity of hydroxyvitamin D3.


July 7, 2019

Complete genome sequence of the Arcobacter bivalviorum type strain LMG 26154.

Arcobacters are routinely recovered from marine environments, and multiple Arcobacter species have been isolated from shellfish. Arcobacter bivalviorum was recovered from mussels collected in the Ebro Delta in northeastern Spain. This report describes the complete whole-genome sequence of the A. bivalviorum type strain LMG 26154 (= F4T = CECT 7835T).


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