Pupylation-dependent and -independent proteasomal degradation in mycobacteria

Bacteria make use of compartmentalizing protease complexes, similar in architecture but not homologous to the eukaryotic proteasome, for the selective and processive removal of proteins. Mycobacteria as members of the actinobacteria harbor proteasomes in addition to the canonical bacterial degradation complexes. Mycobacterial proteasomal degradation, although not essential during normal growth, becomes critical for survival under particular environmental conditions, like, for example, during persistence of the pathogenic Mycobacterium tuberculosis in host macrophages or of environmental mycobacteria under starvation. Recruitment of protein substrates for proteasomal degradation is usually mediated by pupylation, the post-translational modification of lysine side chains with the prokaryotic ubiquitin-like protein Pup. This substrate recruitment strategy is functionally reminiscent of ubiquitination in eukaryotes, but is the result of convergent evolution, relying on chemically and structurally distinct enzymes. Pupylated substrates are recognized by the ATP-dependent proteasomal regulator Mpa that associates with the 20S proteasome core. A pupylation-independent proteasome degradation pathway has recently been discovered that is mediated by the ATP-independent bacterial proteasome activator Bpa (also referred to as PafE), and that appears to play a role under stress conditions. In this review, mechanistic principles of bacterial proteasomal degradation are discussed and compared with functionally related elements of the eukaryotic ubiquitin-proteasome system. Special attention is given to an understanding on the molecular level based on structural and biochemical analysis. Wherever available, discussion of in vivo studies is included to highlight the biological significance of this unusual bacterial degradation pathway

Pupylation-dependent and -independent proteasomal degradation in mycobacteria

Bacteria make use of compartmentalizing protease complexes, similar in architecture but not homologous to the eukaryotic proteasome, for the selective and processive removal of proteins. Mycobacteria as members of the actinobacteria harbor proteasomes in addition to the canonical bacterial degradation complexes. Mycobacterial proteasomal degradation, although not essential during normal growth, becomes critical for survival under particular environmental conditions, like, for example, during persistence of the pathogenic Mycobacterium tuberculosis in host macrophages or of environmental mycobacteria under starvation. Recruitment of protein substrates for proteasomal degradation is usually mediated by pupylation, the post-translational modification of lysine side chains with the prokaryotic ubiquitin-like protein Pup. This substrate recruitment strategy is functionally reminiscent of ubiquitination in eukaryotes, but is the result of convergent evolution, relying on chemically and structurally distinct enzymes. Pupylated substrates are recognized by the ATP-dependent proteasomal regulator Mpa that associates with the 20S proteasome core. A pupylation-independent proteasome degradation pathway has recently been discovered that is mediated by the ATP-independent bacterial proteasome activator Bpa (also referred to as PafE), and that appears to play a role under stress conditions. In this review, mechanistic principles of bacterial proteasomal degradation are discussed and compared with functionally related elements of the eukaryotic ubiquitin-proteasome system. Special attention is given to an understanding on the molecular level based on structural and biochemical analysis. Wherever available, discussion of in vivo studies is included to highlight the biological significance of this unusual bacterial degradation pathway

Beating Naive Bayes at Taxonomic Classification of 16S rRNA Gene Sequences

Naive Bayes classifiers (NBC) have dominated the field of taxonomic classification of amplicon sequences for over a decade. Apart from having runtime requirements that allow them to be trained and used on modest laptops, they have persistently provided class-topping classification accuracy. In this work we compare NBC with random forest classifiers, neural network classifiers, and a perfect classifier that can only fail when different species have identical sequences, and find that in some practical scenarios there is little scope for improving on NBC for taxonomic classification of 16S rRNA gene sequences. Further improvements in taxonomy classification are unlikely to come from novel algorithms alone, and will need to leverage other technological innovations, such as ecological frequency information

Pupylation-dependent and-independent proteasomal degradation in mycobacteria

ISSN:1868-503XISSN:1868-502

Beating Naive Bayes at Taxonomic Classification of 16S rRNA Gene Sequences

Naive Bayes classifiers (NBC) have dominated the field of taxonomic classification of amplicon sequences for over a decade. Apart from having runtime requirements that allow them to be trained and used on modest laptops, they have persistently provided class-topping classification accuracy. In this work we compare NBC with random forest classifiers, neural network classifiers, and a perfect classifier that can only fail when different species have identical sequences, and find that in some practical scenarios there is little scope for improving on NBC for taxonomic classification of 16S rRNA gene sequences. Further improvements in taxonomy classification are unlikely to come from novel algorithms alone, and will need to leverage other technological innovations, such as ecological frequency information.ISSN:1664-302

Genome‐wide interaction screen for Mycobacterium tuberculosis ClpCP protease reveals toxin–antitoxin systems as a major substrate class

In Mycobacterium tuberculosis (Mtb), the Clp protease degradation pathway, mediated by the modular ClpCP and ClpXP protease complexes, is essential for growth and presents an attractive drug target. Employing a bacterial adenylate cyclase two‐hybrid (BACTH) screening approach that we adapted to screen the proteome of an Mtb ORF library, we identify protein interaction partners of the ClpC1 chaperone on a genome‐wide level. Our results demonstrate that bipartite type II toxin–antitoxin (TA) systems represent a major substrate class. Out of the 67 type II TA systems known in Mtb, 25 appear as ClpC1 interaction partners in the BACTH screen, including members of the VapBC, MazEF, and ParDE families, as well as a RelBE member that was identified biochemically. We show that antitoxins of the Vap and Rel families are degraded by ClpCP in vitro. We also demonstrate that ClpCP is responsible for mediating the N‐end rule pathway, since the adaptor protein ClpS supports ClpC‐dependent degradation of an N‐end rule model substrate in vitro.ISSN:1742-464XISSN:1742-465

Prokaryotic Ubiquitin-Like Protein and Its Ligase/Deligase Enyzmes

ISSN:0022-2836ISSN:1089-863

Reproducible acquisition, management and meta-analysis of nucleotide sequence (meta)data using q2-fondue

Motivation The volume of public nucleotide sequence data has blossomed over the past two decades and is ripe for re- and meta-analyses to enable novel discoveries. However, reproducible re-use and management of sequence datasets and associated metadata remain critical challenges. We created the open source Python package q2-fondue to enable user-friendly acquisition, re-use and management of public sequence (meta)data while adhering to open data principles. Results q2-fondue allows fully provenance-tracked programmatic access to and management of data from the NCBI Sequence Read Archive (SRA). Unlike other packages allowing download of sequence data from the SRA, q2-fondue enables full data provenance tracking from data download to final visualization, integrates with the QIIME 2 ecosystem, prevents data loss upon space exhaustion and allows download of (meta)data given a publication library. To highlight its manifold capabilities, we present executable demonstrations using publicly available amplicon, whole genome and metagenome datasets. Availability and implementation q2-fondue is available as an open-source BSD-3-licensed Python package at https://github.com/bokulich-lab/q2-fondue. Usage tutorials are available in the same repository. All Jupyter notebooks used in this article are available under https://github.com/bokulich-lab/q2-fondue-examples. Supplementary information Supplementary data are available at Bioinformatics online.ISSN:1367-4803ISSN:1460-205

Measuring the microbiome: Best practices for developing and benchmarking microbiomics methods

Microbiomes are integral components of diverse ecosystems, and increasingly recognized for their roles in the health of humans, animals, plants, and other hosts. Given their complexity (both in composition and function), the effective study of microbiomes (microbiomics) relies on the development, optimization, and validation of computational methods for analyzing microbial datasets, such as from marker-gene (e.g., 16S rRNA gene) and metagenome data. This review describes best practices for benchmarking and implementing computational methods (and software) for studying microbiomes, with particular focus on unique characteristics of microbiomes and microbiomics data that should be taken into account when designing and testing microbiomics methods.ISSN:2001-037