Building a tRNA thermometer to estimate microbial adaptation to temperature

Because ambient temperature affects biochemical reactions, organisms living in extreme temperature conditions adapt protein composition and structure to maintain biochemical functions. While it is not feasible to experimentally determine optimal growth temperature (OGT) for every known microbial species, organisms adapted to different temperatures have measurable differences in DNA, RNA and protein composition that allow OGT prediction from genome sequence alone. In this study, we built a ‘tRNA thermometer’ model using tRNA sequence to predict OGT. We used sequences from 100 archaea and 683 bacteria species as input to train two Convolutional Neural Network models. The first pairs individual tRNA sequences from different species to predict which comes from a more thermophilic organism, with accuracy ranging from 0.538 to 0.992. The second uses the complete set of tRNAs in a species to predict optimal growth temperature, achieving a maximum ${r^2}$ of 0.86; comparable with other prediction accuracies in the literature despite a significant reduction in the quantity of input data. This model improves on previous OGT prediction models by providing a model with minimum input data requirements, removing laborious feature extraction and data preprocessing steps and widening the scope of valid downstream analyses.

Bioplastikproduktion mithilfe eines extremophilen kathodischen Biofilms

As the atmospheric CO2 concentrations are increasing, its usage as biotechnological substrate becomes a focus area of applied scientists. As a rather new technique to energize the process of CO2 fixation, microbial electrosynthesis offers the advantage to establish continuous processes based on a cathodic biofilm that is supplied with electrical energy provided by renewable resources. Here we present the cathodic biofilm growth of Kyrpidia spormannii, a recently isolated thermophilic organism that is naturally capable of producing the biodegradable biopolymer polyhydroxybutyrate (PHB).

Building a tRNA thermometer to access the world’s biochemical diversity

ABSTRACTBecause ambient temperature affects biochemical reactions, organisms living in extreme temperature conditions adapt protein composition and structure to maintain biochemical functions. While it is not feasible to experimentally determine optimal growth temperature (OGT) for every known microbial species, organisms adapted to different temperatures have measurable differences in DNA, RNA, and protein composition that allow OGT prediction from genome sequence alone. In this study, we built a model using tRNA sequence to predict OGT. We used tRNA sequences from 100 archaea and 683 bacteria species as input to train two Convolutional Neural Network models. The first pairs individual tRNA sequences from different species to predict which comes from a more thermophilic organism, with accuracy ranging from 0.538 to 0.992. The second uses the complete set of tRNAs in a species to predict optimal growth temperature, achieving a maximum r2 of 0.86; comparable with other prediction accuracies in the literature despite a significant reduction in the quantity of input data. This model improves on previous OGT prediction models by providing a model with minimum input data requirements, removing laborious feature extraction and data preprocessing steps, and widening the scope of valid downstream analyses.

Characterization of the First Bacterial and Thermostable GDP-Mannose 3,5-Epimerase

GDP-mannose 3,5-epimerase (GM35E) catalyzes the conversion of GDP-mannose towards GDP-l-galactose and GDP-l-gulose. Although this reaction represents one of the few enzymatic routes towards the production of l-sugars and derivatives, it has not yet been exploited for that purpose. One of the reasons is that so far only GM35Es from plants have been characterized, yielding biocatalysts that are relatively unstable and difficult to express heterologously. Through the mining of sequence databases, we succeeded in identifying a promising bacterial homologue. The gene from the thermophilic organism Methylacidiphilum fumariolicum was codon optimized for expression in Escherichia coli, resulting in the production of 40 mg/L of recombinant protein. The enzyme was found to act as a self-sufficient GM35E, performing three chemical reactions in the same active site. Furthermore, the biocatalyst was highly stable at temperatures up to 55 °C, making it well suited for the synthesis of new carbohydrate products with application in the pharma industry.

Thermochelin, a Hydroxamate Siderophore from Thermocrispum agreste DSM 44070

Siderophores are produced by microorganisms in iron-deficient environments. They are classified by structure as hydroxamate, catecholate, carboxylate or mixed type siderophores. These differences are also reflected in the selectivity for other valuable elements than iron, which allows designating them as “metallophores”, and makes them of interest for several industrial and medical applications. Thus, it is essential to understand the biosynthesis of these molecules to increase the set of available metallophores that are stable and suited for the respective applications. The probable structure of the metallophore from T. agreste DSM 44070 was predicted by similarity search and gene annotation. An N-hydroxylating monooxygenase (NMO: TheA) of T. agreste DSM 44070 that catalyzes an initial step was synthesized and characterized in detail. The respective metallophore was synthesized, purified and studied. The structure prediction suggested a hydroxamate-type (Erythrochelin-like) metallophore that contains L-N5-hydroxyornithine. This precursor is synthesized by TheA. The siderophore designated as “Thermochelin” is produced, extracted and purified successfully. Complexation was confirmed by CAS-assay. In this study, we expanded the scope of siderophores and the knowledge towards their biosynthetic pathways. Thermochelin is the second siderophore, which was purified from a thermophilic organism, and TheA is the first NMO, which was characterized from an extremophile.

Draft Genome Sequence of Ardenticatena maritima 110S, a Thermophilic Nitrate- and Iron-Reducing Member of the Chloroflexi Class Ardenticatenia

We report here the draft genome sequence of Ardenticatena maritima 110S, the first sequenced member of class Ardenticatenia of the phylum Chloroflexi . This thermophilic organism is capable of a range of physiologies, including aerobic respiration and iron reduction. It also encodes a complete denitrification pathway with a novel nitric oxide reductase.