Intracellular pathways for lignin catabolism in white-rot fungi.

Lignin is a biopolymer found in plant cell walls that accounts for 30% of the organic carbon in the biosphere. White-rot fungi (WRF) are considered the most efficient organisms at degrading lignin in nature. While lignin depolymerization by WRF has been extensively studied, the possibility that WRF are able to utilize lignin as a carbon source is still a matter of controversy. Here, we employ 13C-isotope labeling, systems biology approaches, and in vitro enzyme assays to demonstrate that two WRF, Trametes versicolor and Gelatoporia subvermispora, funnel carbon from lignin-derived aromatic compounds into central carbon metabolism via intracellular catabolic pathways. These results provide insights into global carbon cycling in soil ecosystems and furthermore establish a foundation for employing WRF in simultaneous lignin depolymerization and bioconversion to bioproducts-a key step toward enabling a sustainable bioeconomy.

Identification and expression of the 11ß-steroid hydroxylase from Cochliobolus lunatus in Corynebacterium glutamicum.

Hydroxylation of steroids has acquired special relevance for the pharmaceutical industries. Particularly, the 11ß-hydroxylation of steroids is a reaction of biotechnological importance currently carried out at industrial scale by the fungus Cochliobolus lunatus. In this work, we have identified the genes encoding the cytochrome CYP103168 and the reductase CPR64795 of C. lunatus responsible for the 11ß-hydroxylase activity in this fungus, which is the key step for the preparative synthesis of cortisol in industry. A recombinant Corynebacterium glutamicum strain harbouring a plasmid expressing both genes forming a synthetic bacterial operon was able to 11ß-hydroxylate several steroids as substrates. This is a new example to show that the industrial strain C. glutamicum can be used as a suitable chassis to perform steroid biotransformation expressing eukaryotic cytochromes.

Genome sequence and characterization of the bcs clusters for the production of nanocellulose from the low pH resistant strain Komagataeibacter medellinensis ID13488.

Komagataeibacter medellinensis ID13488 (formerly Gluconacetobacter medellinensis ID13488) is able to produce crystalline bacterial cellulose (BC) under high acidic growth conditions. These abilities make this strain desirable for industrial BC production from acidic residues (e.g. wastes generated from cider production). To explore the molecular bases of the BC biosynthesis in this bacterium, the genome has been sequenced revealing a sequence of 3.4 Mb containing three putative plasmids of 38.1 kb (pKM01), 4.3 kb (pKM02) and 3.3 Kb (pKM03). Genome comparison analyses of K. medellinensis ID13488 with other cellulose-producing related strains resulted in the identification of the bcs genes involved in the cellulose biosynthesis. Genes arrangement and composition of four bcs clusters (bcs1, bcs2, bcs3 and bcs4) was studied by RT-PCR, and their organization in four operons transcribed as four independent polycistronic mRNAs was determined. qRT-PCR experiments demonstrated that mostly bcs1 and bcs4 are expressed under BC production conditions, suggesting that these operons direct the synthesis of BC. Genomic differences with the close related strain K. medellinensis NBRC 3288 unable to produce BC were also described and discussed.

In silico prospection of microorganisms to produce polyhydroxyalkanoate from whey: Caulobacter segnis DSM 29236 as a suitable industrial strain.

Polyhydroxyalkanoates (PHAs) are polyesters of microbial origin that can be synthesized by prokaryotes from noble sugars or lipids and from complex renewable substrates. They are an attractive alternative to conventional plastics because they are biodegradable and can be produced from renewable resources, such as the surplus of whey from dairy companies. After an in silico screening to search for ß-galactosidase and PHA polymerase genes, several bacteria were identified as potential PHA producers from whey based on their ability to hydrolyse lactose. Among them, Caulobacter segnis DSM 29236 was selected as a suitable strain to develop a process for whey surplus valorization. This microorganism accumulated 31.5% of cell dry weight (CDW) of poly(3-hydroxybutyrate) (PHB) with a titre of 1.5 g l-1 in batch assays. Moreover, the strain accumulated 37% of CDW of PHB and 9.3 g l-1 in fed-batch mode of operation. This study reveals this species as a PHA producer and experimentally validates the in silico bioprospecting strategy for selecting microorganisms for waste re-valorization.

Complete mitochondrial genome of Polymastia littoralis (Demospongiae, Polymastiidae).

The complete mitochondrial genome of Polymastia littoralis (Demospongiae, Polymastiidae) is reported here for the first time. The P. littoralis mitogenome is 21,719 bp base pairs in total length and includes 14 protein-coding gene sequences, small and large rRNA sequences, and 25 tRNA sequences. All genes are encoded on the heavy strand. There are two overlapping genes trnE and nad6.

Whole-genome analysis of Azoarcus sp. strain CIB provides genetic insights to its different lifestyles and predicts novel metabolic features.

The genomic features of Azoarcus sp. CIB reflect its most distinguishing phenotypes as a diazotroph, facultative anaerobe, capable of degrading either aerobically and/or anaerobically a wide range of aromatic compounds, including some toxic hydrocarbons such as toluene and m-xylene, as well as its endophytic lifestyle. The analyses of its genome have expanded the catabolic potential of strain CIB toward common natural compounds, such as certain diterpenes, that were not anticipated as carbon sources. The high number of predicted solvent efflux pumps and heavy metal resistance gene clusters has provided the first evidence for two environmentally relevant features of this bacterium that remained unknown. Genome mining has revealed several gene clusters likely involved in the endophytic lifestyle of strain CIB, opening the door to the molecular characterization of some plant growth promoting traits. Horizontal gene transfer and mobile genetic elements appear to have played a major role as a mechanism of adaptation of this bacterium to different lifestyles. This work paves the way for a systems biology-based understanding of the abilities of Azoarcus sp. CIB to integrate aerobic and anaerobic metabolism of aromatic compounds, tolerate stress conditions, and interact with plants as an endophyte of great potential for phytostimulation and phytoremediation strategies. Comparative genomics provides an Azoarcus pan genome that confirms the global metabolic flexibility of this genus, and suggests that its phylogeny should be revisited.

Genome Sequence of Pseudomonas azelaica Strain Aramco J.

We report here the draft genome sequence of Pseudomonas azelaica strain Aramco J (7.3 Mbp; GC content, 61.9%), one of the few bacteria that can completely mineralize different hydroxybiphenyls, e.g., 2-hydroxybiphenyl, 2,2'-dihydroxybiphenyl, and 3-hydroxybiphenyl. The findings obtained from its genome annotation suggest that this strain becomes a useful biocatalyst for aromatic bioconversions.

Draft Genome Sequence of Actinoplanes utahensis NRRL 12052, a Microorganism Involved in Industrial Production of Pharmaceutical Intermediates.

Here, we describe the draft genome sequence of Actinoplanes utahensis NRRL 12052, a filamentous bacterium that encodes an aculeacin A acylase and a putative N-acyl-homoserine lactone acylase of biotechnological interest. Moreover, several nonribosomal peptide synthase (NRPS) and polyketide synthase (PKS) clusters and antibiotic resistance genes have been identified.

Genome Sequence of Pseudomonas azelaica HBP1, Which Catabolizes 2-Hydroxybiphenyl Fungicide.

Pseudomonas azelaica HBP1 (DSM 8897) is one of the few bacteria able to completely mineralize the 2-hydroxybiphenyl biocide. Here, we report the draft genome sequence of this strain (7.4 Mbp; G+C content, 63.5%) and the findings obtained from its genome annotation.

Genome Sequence of Streptomyces exfoliatus DSMZ 41693, a Source of Poly(3-Hydroxyalkanoate)-Degrading Enzymes.

Here we report the draft genome sequence of Streptomyces exfoliatus DSMZ 41693, which includes a gene encoding a poly(3-hydroxyoctanoate) depolymerase, an enzyme which can be used for the industrial synthesis of chiral (R)-3-hydroxyalkanoic acids. In addition, the genome carries numerous genes involved in the biosynthesis of secondary metabolites, including polyketides and terpenes.

Genome of the Psychrophilic Bacterium Bacillus psychrosaccharolyticus, a Potential Source of 2'-Deoxyribosyltransferase for Industrial Nucleoside Synthesis.

Here we report the draft genome sequence of Bacillus psychrosaccharolyticus, a cold-adapted bacterium with biotechnological interest. The genome contains genes related to the ability of this microorganism to grow at low temperatures and includes a nucleoside 2'-deoxyribosyltransferase, which can be used in the industrial synthesis of modified nucleosides with therapeutic activity.

Genome Sequence of the Butanol Hyperproducer Clostridium saccharoperbutylacetonicum N1-4.

Clostridium saccharoperbutylacetonicum is one of the most important acetone-butanol-ethanol (ABE)-generating industrial microorganisms and one of the few bacteria containing choline in its cell wall. Here, we report the draft genome sequence of C. saccharoperbutylacetonicum strain N1-4 (6.6 Mbp; G+C content, 29.4%) and the findings obtained from the annotation of the genome.

Genome sequence of the methanotrophic poly-ß-hydroxybutyrate producer Methylocystis parvus OBBP.

Methylocystis parvus OBBP is an obligate methylotroph considered the type species of the genus Methylocystis. Two pmoCAB particulate methane monooxygenase operons and one additional singleton pmoC paralog were identified in the sequence. No evidence of genes encoding soluble methane monooxygenase was found. Comparison of M. parvus OBBP and Methylocystis sp. strain Rockwell (ATCC 49242) suggests that both species should be taxonomically classified in different genera.