The Draft Genome Sequence of Thermophilic Thermoanaerobacterium thermosaccharolyticum M5 Capable of Directly Producing Butanol from Hemicellulose

Report of genome sequence of Rhodococcus biphenylivorans strain GA1, an isolate capable of efficiently degrading lignin and its derivates

Rhodococcus biphenylivorans GA1 was successfully isolated, which can efficiently degrade alkali lignin and a variety of lignin-derived aromatic compounds as the sole carbon source. Whole genome sequencing of strain GA1 showed that it possessed G + C content of 68% with the size of 6.0 Mb and 4319 putative open reading frames (ORFs). Four replicons consisting of one circular chromosome (ChrA1) and three circular plasmids (pGA1, pGA2, pGA3) were found. Among these annotated proteins, lignin depolymerizing peroxidases (Dyp) and two lignin-derived aromatic compounds cleavage dioxygenases, protocatechuate 3,4-dioxygenase(P34D) and catechol-1,2-dioxygenase (C12D) play key roles in the catabolism of lignin.

Breeding of a thermostable xylanase-producing strain of Myceliophthora thermophila by atmospheric room temperature plasma (ARTP) mutagenesis

Introduction: Hemicellulose is an important component in lignocellulose materials, which is second only to cellulose, accounting for 15%-35% of the dry weight of plants. In the current situation of energy shortage, making full use of lignocellulose materials to produce fuel ethanol has become an important way to solve the energy problem. Xylanase plays a crucial role in the utilization of hemicellulose. It is a necessary means to reduce the cost of hemicellulose utilization by improving the activity of xylanase. Moreover, most naturally xylanases are mesophilic enzymes, which limits their industrial application. Methods:In this study, Myceliophthora thermophila was used to produce xylanases and a thermostable mutant M 2103 was obtained by atmospheric room temperature plasma (ARTP) mutagenesis. The research work started with exploring the effects of ARTP mutagenesis on the antioxidase system [superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), polyphenol oxidase (PPO), and antioxidant capacity (AOC)] of M. thermophile, and found that superoxide dismutase activity increased by 221.13%, and polyphenol oxidase activity increased by 486.04% as compared with the original strain when the implantation time was 300 s. So as to determine the conditions for subsequent mutagenesis. Results and Discussion:For the mutant M 2103, the reaction temperature for xylanase production remained stable in the range of 70°C-85°C. Its optimum temperature was 75°C, which was 15°C higher than that of the original strain. And its xylanase activity increased by 21.71% as compared with the original strain. M 2103 displayed a significantly higher relative xylanase activity than the original strain in the acidic (pH 4.0-7.0) range, and the xylanase activity was relatively stable in the pH range of 6.0-8.5. These results provide an alternative biocatalyst for the production of xylooligosaccharide, and a potential usage of ARTP in the mutagenesis of thermostable mutant.

The draft genome sequence of Rhodosporidium toruloides strain Z11, an isolate capable of co-producing lipids and carotenoids from waste molasses

A wild-type Rhodosporidium toruloides strain Z11 which could utilize molasses to co-produce high amount of lipid and carotenoids was isolated and characterized. The genome of strain Z11 with a G + C content of 59.0% was estimated to be 22.6 Mb and contained 5290 encoded protein sequences. Among these annotated genes, the ATP citrate (pro-S)-lyase, two malic enzymes (MaeA and MaeB) and the geranylgeranyl pyrophosphate synthase play key roles for the production of lipids and carotenoids. In addition, a β-fructofuranosidase (SacA) was identified, which may contribute to the utilization of molasses.

Expansion segments in bacterial and archaeal 5S ribosomal RNAs

The large ribosomal RNAs of eukaryotes frequently contain expansion sequences that add to the size of the rRNAs but do not affect their overall structural layout and are compatible with major ribosomal function as an mRNA translation machine. The expansion of prokaryotic ribosomal RNAs is much less explored. In order to obtain more insight into the structural variability of these conserved molecules, we herein report the results of a comprehensive search for the expansion sequences in prokaryotic 5S rRNAs. Overall, 89 expanded 5S rRNAs of 15 structural types were identified in 15 archaeal and 36 bacterial genomes. Expansion segments ranging in length from 13 to 109 residues were found to be distributed among 17 insertion sites. The strains harboring the expanded 5S rRNAs belong to the bacterial orders Clostridiales, Halanaerobiales, Thermoanaerobacterales, and Alteromonadales as well as the archael order Halobacterales When several copies of a 5S rRNA gene are present in a genome, the expanded versions may coexist with normal 5S rRNA genes. The insertion sequences are typically capable of forming extended helices, which do not seemingly interfere with folding of the conserved core. The expanded 5S rRNAs have largely been overlooked in 5S rRNA databases.

How to outwit nature: Omics insight into butanol tolerance

The energy crisis, depletion of oil reserves, and global climate changes are pressing problems of developed societies. One possibility to counteract that is microbial production of butanol, a promising new fuel and alternative to many petrochemical reagents. However, the high butanol toxicity to all known microbial species is the main obstacle to its industrial implementation. The present state of the art review aims to expound the recent advances in modern omics approaches to resolving this insurmountable to date problem of low butanol tolerance. Genomics, transcriptomics, and proteomics show that butanol tolerance is a complex phenomenon affecting multiple genes and their expression. Efflux pumps, stress and multidrug response, membrane transport, and redox-related genes are indicated as being most important during butanol challenge, in addition to fine-tuning of global regulators of transcription (Spo0A, GntR), which may further improve tolerance. Lipidomics shows that the alterations in membrane composition (saturated lipids and plasmalogen increase) are very much species-specific and butanol-related. Glycomics discloses the pleiotropic effect of CcpA, the role of alternative sugar transport, and the production of exopolysaccharides as alternative routes to overcoming butanol stress. Unfortunately, the strain that simultaneously syntheses and tolerates butanol in concentrations that allow its commercialization has not yet been discovered or produced. Omics insight will allow the purposeful increase of butanol tolerance in natural and engineered producers and the effective heterologous expression of synthetic butanol pathways in strains hereditary butanol-resistant up to 3.2 - 4.9% (w/v). Future breakthrough can be achieved by a detailed study of the membrane proteome, of which 21% are proteins with unknown functions.

The draft genome sequence of Clostridium sp. strain CT7, an isolate capable of producing butanol but not acetone and 1,3-propanediol from crude glycerol

A solventogenic Clostridium sp. strain CT7 which could utilize glycerol directly to produce high yields of butanol was isolated. In the presence of crude glycerol, strain CT7 synthesized butanol through a unique butanol-ethanol (BE) fermentation pathway in which acetone and 1,3-propanediol (1,3-PDO) were not produced. The genome of strain CT7 which has a G + C content of 30.3% was estimated to be 5.99 Mb and contained 4319 putative Open Reading Frames (ORF). The putative annotated genes, which play major roles in BE production from crude glycerol, included glycerol dehydrogenase gene (gdh), acetoacetyl-CoA transferase gene (ctfA/B), and bifunctional alcohol and aldehyde dehydrogenase gene (adhE). In addition, non-typical BE production is not coupled to 1,3-propanediol formation, which may due to the defect of 1, 3-PDO dehydrogenase gene (dhaT).