A Guild of 45 CRISPR-Associated (Cas) Protein Families and Multiple CRISPR/Cas Subtypes Exist in Prokaryotic Genomes

Clustered regularly interspaced short palindromic repeats (CRISPRs) are a family of DNA direct repeats found in many prokaryotic genomes. Repeats of 21–37 bp typically show weak dyad symmetry and are separated by regularly sized, nonrepetitive spacer sequences. Four CRISPR-associated (Cas) protein families, designated Cas1 to Cas4, are strictly associated with CRISPR elements and always occur near a repeat cluster. Some spacers originate from mobile genetic elements and are thought to confer “immunity” against the elements that harbor these sequences. In the present study, we have systematically investigated uncharacterized proteins encoded in the vicinity of these CRISPRs and found many additional protein families that are strictly associated with CRISPR loci across multiple prokaryotic species. Multiple sequence alignments and hidden Markov models have been built for 45 Cas protein families. These models identify family members with high sensitivity and selectivity and classify key regulators of development, DevR and DevS, in Myxococcus xanthus as Cas proteins. These identifications show that CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a repeat cluster or filling the region between two repeat clusters. Distinctive subsets of the collection of Cas proteins recur in phylogenetically distant species and correlate with characteristic repeat periodicity. The analyses presented here support initial proposals of mobility of these units, along with the likelihood that loci of different subtypes interact with one another as well as with host cell defensive, replicative, and regulatory systems. It is evident from this analysis that CRISPR/cas loci are larger, more complex, and more heterogeneous than previously appreciated

Spherical collapse of supermassive stars: neutrino emission and gamma-ray bursts

We present the results of numerical simulations of the spherically symmetric gravitational collapse of supermassive stars (SMS). The collapse is studied using a general relativistic hydrodynamics code. The coupled system of Einstein and fluid equations is solved employing observer time coordinates, by foliating the spacetime by means of outgoing null hypersurfaces. The code contains an equation of state which includes effects due to radiation, electrons and baryons, and detailed microphysics to account for electron-positron pairs. In addition energy losses by thermal neutrino emission are included. We are able to follow the collapse of SMS from the onset of instability up to the point of black hole formation. Several SMS with masses in the range $5\times 10^5 M_{\odot}- 10^9 M_{\odot}$ are simulated. In all models an apparent horizon forms initially, enclosing the innermost 25% of the stellar mass. From the computed neutrino luminosities, estimates of the energy deposition by $\nu\bar{\nu}$-annihilation are obtained. Only a small fraction of this energy is deposited near the surface of the star, where, as proposed recently by Fuller & Shi (1998), it could cause the ultrarelativistic flow believed to be responsible for $\gamma$-ray bursts. Our simulations show that for collapsing SMS with masses larger than $5\times 10^5 M_{\odot}$ the energy deposition is at least two orders of magnitude too small to explain the energetics of observed long-duration bursts at cosmological redshifts. In addition, in the absence of rotational effects the energy is deposited in a region containing most of the stellar mass. Therefore relativistic ejection of matter is impossible.Comment: 13 pages, 11 figures, submitted to A&

Life in Hot Carbon Monoxide: The Complete Genome Sequence of Carboxydothermus hydrogenoformans Z-2901

We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are diverse bacteria and archaea that grow anaerobically utilizing carbon monoxide (CO) as their sole carbon source and water as an electron acceptor, producing carbon dioxide and hydrogen as waste products. Organisms that make use of CO do so through carbon monoxide dehydrogenase complexes. Remarkably, analysis of the genome of C. hydrogenoformans reveals the presence of at least five highly differentiated anaerobic carbon monoxide dehydrogenase complexes, which may in part explain how this species is able to grow so much more rapidly on CO than many other species. Analysis of the genome also has provided many general insights into the metabolism of this organism which should make it easier to use it as a source of biologically produced hydrogen gas. One surprising finding is the presence of many genes previously found only in sporulating species in the Firmicutes Phylum. Although this species is also a Firmicutes, it was not known to sporulate previously. Here we show that it does sporulate and because it is missing many of the genes involved in sporulation in other species, this organism may serve as a “minimal” model for sporulation studies. In addition, using phylogenetic profile analysis, we have identified many uncharacterized gene families found in all known sporulating Firmicutes, but not in any non-sporulating bacteria, including a sigma factor not known to be involved in sporulation previously

Particle dynamics in sheared granular matter

The particle dynamics and shear forces of granular matter in a Couette geometry are determined experimentally. The normalized tangential velocity $V(y)$ declines strongly with distance $y$ from the moving wall, independent of the shear rate and of the shear dynamics. Local RMS velocity fluctuations $\delta V(y)$ scale with the local velocity gradient to the power $0.4 \pm 0.05$. These results agree with a locally Newtonian, continuum model, where the granular medium is assumed to behave as a liquid with a local temperature $\delta V(y)^2$ and density dependent viscosity

GlyGly-CTERM and Rhombosortase: A C-Terminal Protein Processing Signal in a Many-to-One Pairing with a Rhomboid Family Intramembrane Serine Protease

The rhomboid family of serine proteases occurs in all domains of life. Its members contain at least six hydrophobic membrane-spanning helices, with an active site serine located deep within the hydrophobic interior of the plasma membrane. The model member GlpG from Escherichia coli is heavily studied through engineered mutant forms, varied model substrates, and multiple X-ray crystal studies, yet its relationship to endogenous substrates is not well understood. Here we describe an apparent membrane anchoring C-terminal homology domain that appears in numerous genera including Shewanella, Vibrio, Acinetobacter, and Ralstonia, but excluding Escherichia and Haemophilus. Individual genomes encode up to thirteen members, usually homologous to each other only in this C-terminal region. The domain's tripartite architecture consists of motif, transmembrane helix, and cluster of basic residues at the protein C-terminus, as also seen with the LPXTG recognition sequence for sortase A and the PEP-CTERM recognition sequence for exosortase. Partial Phylogenetic Profiling identifies a distinctive rhomboid-like protease subfamily almost perfectly co-distributed with this recognition sequence. This protease subfamily and its putative target domain are hereby renamed rhombosortase and GlyGly-CTERM, respectively. The protease and target are encoded by consecutive genes in most genomes with just a single target, but far apart otherwise. The signature motif of the Rhombo-CTERM domain, often SGGS, only partially resembles known cleavage sites of rhomboid protease family model substrates. Some protein families that have several members with C-terminal GlyGly-CTERM domains also have additional members with LPXTG or PEP-CTERM domains instead, suggesting there may be common themes to the post-translational processing of these proteins by three different membrane protein superfamilies

Avian ecological succession in the Amazon: A long-term case study following experimental deforestation

Approximately 20% of the Brazilian Amazon has now been deforested, and the Amazon is currently experiencing the highest rates of deforestation in a decade, leading to large-scale land-use changes. Roads have consistently been implicated as drivers of ongoing Amazon deforestation and may act as corridors to facilitate species invasions. Long-term data, however, are necessary to determine how ecological succession alters avian communities following deforestation and whether established roads lead to a constant influx of new species. We used data across nearly 40 years from a large-scale deforestation experiment in the central Amazon to examine the avian colonization process in a spatial and temporal framework, considering the role that roads may play in facilitating colonization. Since 1979, 139 species that are not part of the original forest avifauna have been recorded, including more secondary forest species than expected based on the regional species pool. Among the 35 species considered to have colonized and become established, a disproportionate number were secondary forest birds (63%), almost all of which first appeared during the 1980s. These new residents comprise about 13% of the current community of permanent residents. Widespread generalists associated with secondary forest colonized quickly following deforestation, with few new species added after the first decade, despite a stable road connection. Few species associated with riverine forest or specialized habitats colonized, despite road connection to their preferred source habitat. Colonizing species remained restricted to anthropogenic habitats and did not infiltrate old-growth forests nor displace forest birds. Deforestation and expansion of road networks into terra firme rainforest will continue to create degraded anthropogenic habitat. Even so, the initial pulse of colonization by nonprimary forest bird species was not the beginning of a protracted series of invasions in this study, and the process appears to be reversible by forest succession. © 2019 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd

Red giant bound on the axion-electron coupling reexamined

If axions or other low-mass pseudoscalars couple to electrons (``fine structure constant'' $\alpha_a$) they are emitted from red giant stars by the Compton process $\gamma+e\to e+a$ and by bremsstrahlung $e+(Z,A)\to (Z,A)+e+a$. We construct a simple analytic expression for the energy-loss rate for all conditions relevant for a red giant and include axion losses in evolutionary calculations from the main sequence to the helium flash. We find that \alpha_a\lapprox0.5\mn(-26) or m_a\lapprox 9\,\meV/\cos^2\beta lest the red giant core at helium ignition exceed its standard mass by more than 0.025\,\MM_\odot, in conflict with observational evidence. Our bound is the most restrictive limit on $\alpha_a$, but it does not exclude the possibility that axion emission contributes significantly to the cooling of ZZ~Ceti stars such as G117--B15A for which the period decrease was recently measured.Comment: 11 pages, uuencoded and compressed postscript fil