Flashy flagella: flagellin modification is relatively common and highly versatile among the Enterobacteriaceae

Schematic diagrams of inserts within the fliDCAZ loci of FGI−/FMI− Enterobacteriaceae. Flanking genes are indicated by yellow arrows, predicted phage genes by blue arrows, fimbrial biogenesis genes by grey arrows and sugar/amino acid transporter genes by orange arrows. Black arrows indicate predicted transposase or endonuclease genes, while the red arrows indicate genes with disrupted reading frames. The flagellin glycan biosynthetic genes in the FGI+ strains E. tracheiphila Buff/PSU-1 are indicated by green arrows, upstream of the predicted phage integration site. (TIF 471 kb

Not All That Glitters Is Gold: The Paradox of CO-dependent Hydrogenogenesis in Parageobacillus thermoglucosidasius

The thermophilic bacterium Parageobacillus thermoglucosidasius has recently gained interest due to its ability to catalyze the water gas shift reaction, where the oxidation of carbon monoxide (CO) is linked to the evolution of hydrogen (H$_{2}$) gas. This phenotype is largely predictable based on the presence of a genomic region coding for a carbon monoxide dehydrogenase (CODH—Coo) and hydrogen evolving hydrogenase (Phc). In this work, seven previously uncharacterized strains were cultivated under 50% CO and 50% air atmosphere. Despite the presence of the coo—phc genes in all seven strains, only one strain, Kp1013, oxidizes CO and yields H$_{2}$. The genomes of the H$_{2}$ producing strains contain unique genomic regions that code for proteins involved in nickel transport and the detoxification of catechol, a by-product of a siderophore-mediated iron acquisition system. Combined, the presence of these genomic regions could potentially drive biological water gas shift (WGS) reaction in P. thermoglucosidasius

Carbon monoxide induced metabolic shift in the carboxydotrophic parageobacillus thermoglucosidasius dsm 6285

Parageobacillus thermoglucosidasius is known to catalyse the biological water gas shift (WGS) reaction, a pathway that serves as a source of alternative energy and carbon to a wide variety of bacteria. Despite increasing interest in this bacterium due to its ability to produce biological hydrogen through carbon monoxide (CO) oxidation, there are no data on the effect of toxic CO gas on its physiology. Due to its general requirement of O$_{2}$, the organism is often grown aerobically to generate biomass. Here, we show that carbon monoxide (CO) induces metabolic changes linked to distortion of redox balance, evidenced by increased accumulation of organic acids such as acetate and lactate. This suggests that P. thermoglucosidasius survives by expressing several alternative pathways, including conversion of pyruvate to lactate, which balances reducing equivalents (oxidation of NADH to NAD+), and acetyl-CoA to acetate, which directly generates energy, while CO is binding terminal oxidases. The data also revealed clearly that P. thermoglucosidasius gained energy and grew during the WGS reaction. Combined, the data provide critical information essential for further development of the biotechnological potential of P. thermoglucosidasiu

Comparative genomic analysis of the flagellin glycosylation island of the Gram-positive thermophile Geobacillus

BACKGROUND : Protein glycosylation involves the post-translational attachment of sugar chains to target proteins and has been observed in all three domains of life. Post-translational glycosylation of flagellin, the main structural protein of the flagellum, is a common characteristic among many Gram-negative bacteria and Archaea. Several distinct functions have been ascribed to flagellin glycosylation, including stabilisation and maintenance of the flagellar filament, motility, surface recognition, adhesion, and virulence. However, little is known about this trait among Gram-positive bacteria. RESULTS : Using comparative genomic approaches the flagellin glycosylation loci of multiple strains of the Gram-positive thermophilic genus Geobacillus were identified and characterized. Eighteen of thirty-six compared strains of the genus carry these loci, which show evidence of horizontal acquisition. The Geobacillus flagellin glycosylation islands (FGIs) can be clustered into five distinct types, which are predicted to encode highly variable glycans decorated with distinct and heavily modified sugars. CONLUSIONS : Our comparative genomic analyses showed that, while not universal, flagellin glycosylation islands are relatively common among members of the genus Geobacillus and that the encoded flagellin glycans are highly variable. This suggests that flagellin glycosylation plays an important role in the lifestyles of members of this thermophilic genus.PDM was funded by the National Research Foundation of South Africa (Research Career Advancement Fellowship - Grant 91447).http://www.biomedcentral.com/bmcgenomicsam2016Genetic

Genomic insights into the lifestyles, functional capacities and oleagenicity of members of the fungal family Trichosporonaceae

Trichosporonaceae incorporates six genera of physiologically and ecologically diverse fungi including both human pathogenic taxa as well as yeasts of biotechnological interest, especially those oleagenic taxa that accumulate large amounts of single cell oils (SCOs). Here, we have undertaken comparative genomic analysis of thirty-three members of the family with a view to gain insight into the molecular determinants underlying their lifestyles and niche specializations. Phylogenomic analysis revealed potential misidentification of three strains which could impact subsequent analyses. Evaluation of the predicted proteins coding sequences showed that the free-living members of the family harbour greater numbers of carbohydrate active enzymes (CAZYmes), metallo- and serine peptidases compared to their host-associated counterparts. Phylogenies of selected lipid biosynthetic enzymes encoded in the genomes of the studied strains revealed disparate evolutionary histories for some proteins inconsistent with the core genome phylogeny. However, the documented oleagenic members distinctly cluster based on the constitution of the upstream regulatory regions of genes encoding acetyl-CoA carboxylase (ACC), ATP-citrate synthase (ACS) and isocitrate dehydrogenase [NADP] (ICDH), which are among the major proteins in the lipid biosynthetic pathway of these yeasts, suggesting a possible pattern in the regulation of these genes

Acetogenic Fermentation From Oxygen Containing Waste Gas

The microbial production of bulk chemicals from waste gas is becoming a pertinent alternative to industrial strategies that rely on fossil fuels as substrate. Acetogens can use waste gas substrates or syngas (CO, CO$_{2}$, H$_{2}$) to produce chemicals, such as acetate or ethanol, but as the feed gas often contains oxygen, which inhibits acetogen growth and product formation, a cost-prohibitive chemical oxygen removal step is necessary. Here, we have developed a two-phase microbial system to facilitate acetate production using a gas mixture containing CO and O$_{2}$. In the first phase the facultative anaerobic carboxydotroph Parageobacillus thermoglucosidasius was used to consume residual O$_{2}$ and produce H$_{2}$ and CO$_{2}$, which was subsequently utilized by the acetogen Clostridium ljungdahlii for the production of acetate. From a starting amount of 3.3 mmol of CO, 0.52 mmol acetate was produced in the second phase by C. ljungdahlii. In this set-up, the yield achieved was 0.16mol acetate/mol CO, a 63% of the theoretical maximum. This system has the potential to be developed for the production of a broad range of bulk chemicals from oxygen-containing waste gas by using P. thermoglucosidasius as an oxygen scrubbing tool

The genome of the Antarctic polyextremophile Nesterenkonia sp. AN1 reveals adaptive strategies for survival under multiple stress conditions

Nesterenkonia sp. AN1 is a polyextremophile isolated from Antarctic desert soil. Genomic analyses and genome comparisons with three mesophilic Nesterenkonia strains indicated that the unique genome fraction of Nesterenkonia sp. AN1 contains adaptive features implicated in the response to cold stress including modulation of membrane fluidity as well as response to cold-associated osmotic and oxidative stress. The core genome also encodes a number of putative cold stress response proteins. RNA-Seq-based transcriptome analyses of Nesterenkonia sp. AN1 grown at 5 ºC and 21oC showed that there was significant induction of transcripts that code for antioxidants at 5 ºC, demonstrated by the upregulation of sodA, bcp and bpoA2. There was also overexpression of universal stress protein genes related to uspA, along with genes encoding other characterised cold stress features. Genes encoding the two key enzymes of the glyoxylate cycle, isocitrate lyase (ICL) and malate synthase (AceB) were induced at 5 ºC, suggesting possible adaptation strategies for energy metabolism in cold habitats. These genomic features may contribute to the survival of Nesterenkonia sp. AN1 in arid Antarctic soils.National Research Foundation-South African National Antarctic Research Programme (NRF-SANAP) (Award No. 80256).Genomics Research Institute (GRI) University of Pretoria.http://femsre.oxfordjournals.org2017-02-28hb2016GeneticsMicrobiology and Plant Patholog

Reorganising the order Bacillales through phylogenomics

Bacterial classification at higher taxonomic ranks such as the order and family levels is currently reliant on phylogenetic analysis of 16S rRNA and the presence of shared phenotypic characteristics. However, these may not be reflective of the true genotypic and phenotypic relationships of taxa. This is evident in the order Bacillales, members of which are defined as aerobic, spore-forming and rod-shaped bacteria. However, some taxa are anaerobic, asporogenic and coccoid. 16S rRNA gene phylogeny is also unable to elucidate the taxonomic positions of several families incertae sedis within this order. Whole genome-based phylogenetic approaches may provide a more accurate means to resolve higher taxonomic levels. A suite of phylogenomic approaches were applied to re-evaluate the taxonomy of 80 representative taxa of eight families (and six family incertae sedis taxa) within the order Bacillales. This showed several anomalies in the current family and order level classifications including the existence of four Bacillaceae and two Paenibacillaceae “family” clades. Furthermore, the families Staphylococcaceae and Listeriaceae belong to the sister order Lactobacillales. Finally, we propose a consensus phylogenomic approach which may diminish algorithmic biases associated with single approaches and facilitate more accurate classification of a broad range of taxa at the higher taxonomic levels.PDM acknowledges funding from the University of the Witwatersrand Faculty Research Council (FRC) and HA acknowledges the University of Pretoria for postdoctoral funding.http://www.elsevier.de/syapm2020-03-01hj2019Genetic

Comparative analysis of the Geobacillus hemicellulose utilization locus reveals a highly variable target for improved hemicellulolysis

BACKGROUND: Members of the thermophilic genus Geobacillus can grow at high temperatures and produce a battery of thermostable hemicellulose hydrolytic enzymes, making them ideal candidates for the bioconversion of biomass to value-added products. To date the molecular determinants for hemicellulose degradation and utilization have only been identified and partially characterized in one strain, namely Geobacillus stearothermophilus T-6, where they are clustered in a single genetic locus. RESULTS: Using the G. stearothermophilus T-6 hemicellulose utilization locus as genetic marker, orthologous hemicellulose utilization (HUS) loci were identified in the complete and partial genomes of 17/24 Geobacillus strains. These HUS loci are localized on a common genomic island. Comparative analyses of these loci revealed extensive variability among the Geobacillus hemicellulose utilization systems, with only seven out of 41–68 proteins encoded on these loci conserved among the HUS+ strains. This translates into extensive differences in the hydrolytic enzymes, transport systems and metabolic pathways employed by Geobacillus spp. to degrade and utilize hemicellulose polymers. CONCLUSIONS: The genetic variability among the Geobacillus HUS loci implies that they have variable capacities to degrade hemicellulose polymers, or that they may degrade distinct polymers, as are found in different plant species and tissues. The data from this study can serve as a basis for the genetic engineering of a Geobacillus strain(s) with an improved capacity to degrade and utilize hemicellulose.This project was partially funded through the University of Pretoria Postdoctoral Fellowship Programme and the National Research Foundation (NRF) Research Career Advancement (RCA) Fellowship Programme.http://www.biomedcentral.com/bmcgenomics/am201

Comparative genomic analysis of the secondary flagellar (flag-2) system in the order Enterobacterales

BACKGROUND : The order Enterobacterales encompasses a broad range of metabolically and ecologically versatile bacterial taxa, most of which are motile by means of peritrichous flagella. Flagellar biosynthesis has been linked to a primary flagella locus, flag-1, encompassing ~ 50 genes. A discrete locus, flag-2, encoding a distinct flagellar system, has been observed in a limited number of enterobacterial taxa, but its function remains largely uncharacterized. RESULTS : Comparative genomic analyses showed that orthologous flag-2 loci are present in 592/4028 taxa belonging to 5/8 and 31/76 families and genera, respectively, in the order Enterobacterales. Furthermore, the presence of only the outermost flag-2 genes in many taxa suggests that this locus was far more prevalent and has subsequently been lost through gene deletion events. The flag-2 loci range in size from ~ 3.4 to 81.1 kilobases and code for between five and 102 distinct proteins. The discrepancy in size and protein number can be attributed to the presence of cargo gene islands within the loci. Evolutionary analyses revealed a complex evolutionary history for the flag-2 loci, representing ancestral elements in some taxa, while showing evidence of recent horizontal acquisition in other enterobacteria. CONCLUSIONS : The flag-2 flagellar system is a fairly common, but highly variable feature among members of the Enterobacterales. Given the energetic burden of flagellar biosynthesis and functioning, the prevalence of a second flagellar system suggests it plays important biological roles in the enterobacteria and we postulate on its potential role as locomotory organ or as secretion system.Additional file 1: Table S1. Presence/absence of flag-2 loci among 4028 strains belonging to eight families and 72 genera. The presence of flag-1 loci is also indicated. The previous taxonomy denotes the taxonomy according to the NCBI genome database, while the current taxonomy is according to the Genome Taxonomy Database (GTDB). The isolation source as well as habitat/lifestyles of the different strains are given. Table S2. Molecular characteristics of the flag-2 loci among 592 taxa in the Enterobacterales. The sizes of the flag-2 loci, variable regions VR1 and VR2, their G + C contents (%) and G + C deviation (%) from the genome are shown. The number of predicted proteins encoded on each of these flag-2 fractions are also shown. Table S3. Characteristics of the cargo genes encoded in the variable regions VR1 and VR2 and elsewhere in the enterobacterial flag-2 loci. The number of strains and the families/ genera in which each protein occurs within the flag-2 loci are indicated, as well as the average amino acid identities among enterobacterial orthologues. Conserved domains present in each cargo protein as determined by BlastP analysis against the Conserved Domain Database are shown.The National Research Foundation of South Africahttps://bmcgenomics.biomedcentral.comam2020Forestry and Agricultural Biotechnology Institute (FABI