23 research outputs found
Comprehensive classification of the PIN domain-like superfamily
PIN-like domains constitute a widespread superfamily of nucleases, diverse in terms of the reaction mechanism, substrate specificity, biological function and taxonomic distribution. Proteins with PIN-like domains are involved in central cellular processes, such as DNA replication and repair, mRNA degradation, transcription regulation and ncRNA maturation. In this work, we identify and classify the most complete set of PIN-like domains to provide the first comprehensive analysis of sequence–structure–function relationships within the whole PIN domain-like superfamily. Transitive sequence searches using highly sensitive methods for remote homology detection led to the identification of several new families, including representatives of Pfam (DUF1308, DUF4935) and CDD (COG2454), and 23 other families not classified in the public domain databases. Further sequence clustering revealed relationships between individual sequence clusters and showed heterogeneity within some families, suggesting a possible functional divergence. With five structural groups, 70 defined clusters, over 100,000 proteins, and broad biological functions, the PIN domain-like superfamily constitutes one of the largest and most diverse nuclease superfamilies. Detailed analyses of sequences and structures, domain architectures, and genomic contexts allowed us to predict biological function of several new families, including new toxin-antitoxin components, proteins involved in tRNA/rRNA maturation and transcription/translation regulation
Systematic classification of the His-Me finger superfamily
The His-Me finger endonucleases, also known as
HNH or -metal endonucleases, form a large and
diverse protein superfamily. The His-Me finger domain
can be found in proteins that play an essential
role in cells, including genome maintenance, intron
homing, host defense and target offense. Its overall
structural compactness and non-specificity make
it a perfectly-tailored pathogenic module that participates
on both sides of inter- and intra-organismal
competition. An extremely low sequence similarity
across the superfamily makes it difficult to identify
and classify new His-Me fingers. Using state-of-theart
distant homology detection methods, we provide
an updated and systematic classification of His-Me
finger proteins. In this work, we identified over 100
000 proteins and clustered them into 38 groups, of
which three groups are new and cannot be found in
any existing public domain database of protein families.
Based on an analysis of sequences, structures,
domain architectures, and genomic contexts, we provide
a careful functional annotation of the poorly
characterized members of this superfamily. Our results
may inspire further experimental investigations
that should address the predicted activity and clarify
the potential substrates, to provide more detailed insights
into the fundamental biological roles of these
proteins
Expanding Diversity of Firmicutes Single-Strand Annealing Proteins: a Putative Role of Bacteriophage-Host Arms Race
Bacteriophage-encoded single strand annealing proteins (SSAPs) are recombinases
which can substitute the classical, bacterial RecA and manage the DNA metabolism
at different steps of phage propagation. SSAPs have been shown to efficiently promote
recombination between short and rather divergent DNA sequences and were exploited
for in vivo genetic engineering mainly in Gram-negative bacteria. In opposition to the
conserved and almost universal bacterial RecA protein, SSAPs display great sequence
diversity. The importance for SSAPs in phage biology and phage-bacteria evolution is
underlined by their role as key players in events of horizontal gene transfer (HGT). All
of the above provoke a constant interest for the identification and study of new phage
recombinase proteins in vivo, in vitro as well as in silico. Despite this, a huge body
of putative ssap genes escapes conventional classification, as they are not properly
annotated. In this work, we performed a wide-scale identification, classification and
analysis of SSAPs encoded by the Firmicutes bacteria and their phages. By using
sequence similarity network and gene context analyses, we created a new high quality
dataset of phage-related SSAPs, substantially increasing the number of annotated
SSAPs. We classified the identified SSAPs into seven distinct families, namely RecA,
Gp2.5, RecT/Redb, Erf, Rad52/22, Sak3, and Sak4, organized into three superfamilies.
Analysis of the relationships between the revealed protein clusters led us to recognize
Sak3-like proteins as a new distinct SSAP family. Our analysis showed an irregular
phylogenetic distribution of ssap genes among different bacterial phyla and specific
phages, which can be explained by the high rates of ssap HGT. We propose that
the evolution of phage recombinases could be tightly linked to the dissemination
of bacterial phage-resistance mechanisms (e.g., abortive infection and CRISPR/Cas
systems) targeting ssap genes and be a part of the constant phage-bacteria arms race
The Empirical Correlation between Hydrogen Bonding Strength and Excited-State Intramolecular Proton Transfer in 2-Pyridyl Pyrazoles
The architecture of Tetrahymena telomerase holoenzyme
Telomerase adds telomeric repeats to chromosome ends using an internal RNA template and specialized telomerase reverse transcriptase (TERT), thereby maintaining genome integrity. Little is known about the physical relationships among protein and RNA subunits within a biologically functional holoenzyme. Here we describe the architecture of Tetrahymena thermophila telomerase holoenzyme determined by electron microscopy. Six of the 7 proteins and the TERT-binding regions of telomerase RNA (TER) have been localized by affinity labeling. Fitting with high-resolution structures reveals the organization of TERT, TER, and p65 in the RNP catalytic core. p50 has an unanticipated role as a hub between the RNP catalytic core, p75-p19-p45 subcomplex, and the DNA-binding Teb1. A complete in vitro holoenzyme reconstitution assigns function to these interactions in processive telomeric repeat synthesis. These studies provide the first view of the extensive network of subunit associations necessary for telomerase holoenzyme assembly and physiological function
MEC-17 is an α-tubulin acetyltransferase
In most eukaryotic cells, subsets of microtubules are adapted for specific functions by post-translational modifications (PTMs) of tubulin subunits. Acetylation of the ε-amino group of K40 on α-tubulin is a conserved PTM on the luminal side of microtubules1 that was discovered in the flagella of Chlamydomonas reinhardtii2,3. Studies on the significance of microtubule acetylation have been limited by the undefined status of the α-tubulin acetyltransferase. Here, we show that MEC-17, a protein related to the Gcn5 histone acetyltransferases4 and required for the function of touch receptor neurons in C. elegans5,6, acts as a K40-specific acetyltransferase for α-tubulin. In vitro, MEC-17 exclusively acetylates K40 of α-tubulin. Disruption of the Tetrahymena MEC-17 gene phenocopies the K40R α-tubulin mutation and makes microtubules more labile. Depletion of MEC-17 in zebrafish produces phenotypes consistent with neuromuscular defects. In C. elegans, MEC-17 and its paralog W06B11.1 are redundantly required for acetylation of MEC-12 α-tubulin, and contribute to the function of touch receptor neurons partly via MEC-12 acetylation and partly via another function, possibly by acetylating another protein. In summary, we identify MEC-17 as an enzyme that acetylates the K40 residue of α-tubulin, the only PTM known to occur on the luminal surface of microtubules