Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus

Clustered regularly interspaced short palindromic repeats (CRISPR) are hypervariable loci widely distributed in prokaryotes that provide acquired immunity against foreign genetic elements. Here, we characterize a novel Streptococcus thermophilus locus, CRISPR3, and experimentally demonstrate its ability to integrate novel spacers in response to bacteriophage. Also, we analyze CRISPR diversity and activity across three distinct CRISPR loci in several S. thermophilus strains. We show that both CRISPR repeats and cas genes are locus specific and functionally coupled. A total of 124 strains were studied, and 109 unique spacer arrangements were observed across the three CRISPR loci. Overall, 3,626 spacers were analyzed, including 2,829 for CRISPR1 (782 unique), 173 for CRISPR2 (16 unique), and 624 for CRISPR3 (154 unique). Sequence analysis of the spacers revealed homology and identity to phage sequences (77%), plasmid sequences (16%), and S. thermophilus chromosomal sequences (7%). Polymorphisms were observed for the CRISPR repeats, CRISPR spacers, cas genes, CRISPR motif, locus architecture, and specific sequence content. Interestingly, CRISPR loci evolved both via polarized addition of novel spacers after exposure to foreign genetic elements and via internal deletion of spacers. We hypothesize that the level of diversity is correlated with relative CRISPR activity and propose that the activity is highest for CRISPR1, followed by CRISPR3, while CRISPR2 may be degenerate. Globally, the dynamic nature of CRISPR loci might prove valuable for typing and comparative analyses of strains and microbial populations. Also, CRISPRs provide critical insights into the relationships between prokaryotes and their environments, notably the coevolution of host and viral genomes.     

Post genome-wide association studies of novel genes associated with type 2 diabetes show gene-gene interaction and high predictive value

Background

Recently, several Genome Wide Association (GWA) studies in populations of European descent have identified and validated novel single nucleotide polymorphisms (SNPs), highly associated with type 2 diabetes (T2D). Our aims were to validate these markers in other European and non-European populations, then to assess their combined effect in a large French study comparing T2D and normal glucose tolerant (NGT) individuals.

Methodology/Principal Findings

In the same French population analyzed in our previous GWA study (3,295 T2D and 3,595 NGT), strong associations with T2D were found for CDKAL1 (OR_rs7756992 = 1.30[1.19–1.42], P = 2.3×10⁻⁹), CDKN2A/2B (OR_rs10811661 = 0.74[0.66–0.82], P = 3.5×10⁻⁸) and more modestly for IGFBP2 (OR_rs1470579 = 1.17[1.07–1.27], P = 0.0003) SNPs. These results were replicated in both Israeli Ashkenazi (577 T2D and 552 NGT) and Austrian (504 T2D and 753 NGT) populations (except for CDKAL1) but not in the Moroccan population (521 T2D and 423 NGT). In the overall group of French subjects (4,232 T2D and 4,595 NGT), IGFBP2 and CXCR4 synergistically interacted with (LOC38776, SLC30A8, HHEX) and (NGN3, CDKN2A/2B), respectively, encoding for proteins presumably regulating pancreatic endocrine cell development and function. The T2D risk increased strongly when risk alleles, including the previously discovered T2D-associated TCF7L2 rs7903146 SNP, were combined (8.68-fold for the 14% of French individuals carrying 18 to 30 risk alleles with an allelic OR of 1.24). With an area under the ROC curve of 0.86, only 15 novel loci were necessary to discriminate French individuals susceptible to develop T2D.

Conclusions/Significance

In addition to TCF7L2, SLC30A8 and HHEX, initially identified by the French GWA scan, CDKAL1, IGFBP2 and CDKN2A/2B strongly associate with T2D in French individuals, and mostly in populations of Central European descent but not in Moroccan subjects. Genes expressed in the pancreas interact together and their combined effect dramatically increases the risk for T2D, opening avenues for the development of genetic prediction tests.     

Triterpenoid saponins from Hydrocotyle bonariensis Lam

Phytochemical investigation of the under-ground parts of Hydrocotyle bonariensis led to the isolation of five oleanane-type triterpenoid saponins, 3-O-{β-D-glucopyranosyl-(1 → 2)-[α-L-arabinopyranosyl-(1 → 3)]-β-D-glucuronopyranosyl}-21-O-(2-methylbutyroyl)-22-O-acetyl-R(1)-barrigenol, 3-O-{β-D-glucopyranosyl-(1 → 2)-[α-L-arabinopyranosyl-(1 → 3)]-β-D-glucuronopyranosyl}-21-O-(2-methylbutyroyl)-28-O-acetyl-R(1)-barrigenol, 3-O-{β-D-glucopyranosyl-(1 → 2)-[α-L-arabinopyranosyl-(1 → 3)]-β-D-glucuronopyranosyl}-21-O-acetyl-R(1)-barrigenol, 3-O-{β-D-glucopyranosyl-(1 → 2)-[α-L-arabinopyranosyl-(1 → 3)]-β-D-glucuronopyranosyl}-R(1)-barrigenol, and 3-O-{β-D-glucopyranosyl-(1 → 2)-[α-L-arabinopyranosyl-(1 → 3)]-β-D-glucuronopyranosyl}-22-O-(2-methylbutyroyl)-A(1)-barrigenol, together with the known saniculoside-R1. Their structures were established by 2D NMR techniques and mass spectrometry. Six compounds were evaluated against two human colon cancer cell lines, HCT 116 and HT-29. Two compounds showed weak cytotoxicity with IC(50) 24.1 and 24.0, 83.0 and 83.6 μM against HT-29 and HCT 116, respectively.     

Interrelationships Between Bones,Muscles, and Performance: Biting in the Lizard Tupinambis merianae

The origins of and potential constraints on the evolution of phenotypic diversity remain one of the central questions in evolutionary biology. The vertebrate skeleton is governed by historical, developmental, architectural, and functional constraints that all play a role in establishing its final form. Whereas the factors underlying shape variation in single bones are fairly well understood, this is less so the case for complex assemblages of bones as observed in the cranium or mandible. It is often suggested that the final phenotype must reflect the mechanical constraints imposed by the loading of the skeleton as bones remodel to withstand loading. Yet, in the cranium, in contrast to the mandible, the final phenotype is likely constrained by demands other than loading including the protection of sensory systems and the brain. Architectural design constraints may further limit the final form of complex units like the vertebrate cranium. Here we use geometric morphometric approaches to quantify the shape of the cranium and mandible in a lizard and test whether the observed shape co-varies with both the muscles attaching to these structures as well as functional traits such as bite force. Our results show that co-variation between the cranium and mandible is significant and likely driven by the muscles that link the two systems. Moreover, our results show that the patterns of co-variation are stronger between the mandible and ventral side of the cranium. Muscular cross sectional areas, bite force, and the ventral side of the cranium, also co-vary more than the dorsal side of the cranium does with muscle properties and function. Finally, our results show sex-specific patterns of co-variation with males showing a stronger degree of integration between the cranium, mandible, muscles and bite force suggesting that constraints on bite force drive the evolution of cranial shape to a greater extent in males compared to females.     

Comparative genomics of first available bovine Anaplasma phagocytophilum genome obtained with targeted sequence capture

Background

Anaplasma phagocytophilum is a zoonotic and obligate intracellular bacterium transmitted by ticks. In domestic ruminants, it is the causative agent of tick-borne fever, which causes significant economic losses in Europe. As A. phagocytophilum is difficult to isolate and cultivate, only nine genome sequences have been published to date, none of which originate from a bovine strain.Our goals were to; 1/ develop a sequencing methodology which efficiently circumvents the difficulties associated with A. phagocytophilum isolation and culture; 2/ describe the first genome of a bovine strain; and 3/ compare it with available genomes, in order to both explore key genomic features at the species level, and to identify candidate genes that could be specific to bovine strains.

Results

DNA was extracted from a bovine blood sample infected by A. phagocytophilum. Following a whole genome capture approach, A. phagocytophilum DNA was enriched 197-fold in the sample and then sequenced using Illumina technology. In total, 58.9% of obtained reads corresponded to the A. phagocytophilum genome, covering 85.3% of the HZ genome. Then by performing comparisons with nine previously-sequenced A. phagocytophilum genomes, we determined the core genome of these ten strains. Following analysis, 1281 coding DNA sequences, including 1001 complete sequences, were detected in the A. phagocytophilum bovine genome, of which four appeared to be unique to the bovine isolate. These four coding DNA sequences coded for "hypothetical proteins of unknown function” and require further analysis. We also identified nine proteins common to both European domestic ruminants tested.

Conclusion

Using a whole genome capture approach, we have sequenced the first A. phagocytophilum genome isolated from a cow. To the best of our knowledge, this is the first time that this method has been used to selectively enrich pathogenic bacterial DNA from samples also containing host DNA. The four proteins unique to the A. phagocytophilum bovine genome could be involved in host tropism, therefore their functions need to be explored.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-973) contains supplementary material, which is available to authorized users.     

iLIR database: A web resource for LIR motif-containing proteins in eukaryotes

Atg8-family proteins are the best-studied proteins of the core autophagic machinery. They are essential for the elongation and closure of the phagophore into a proper autophagosome. Moreover, Atg8-family proteins are associated with the phagophore from the initiation of the autophagic process to, or just prior to, the fusion between autophagosomes with lysosomes. In addition to their implication in autophagosome biogenesis, they are crucial for selective autophagy through their ability to interact with selective autophagy receptor proteins necessary for the specific targeting of substrates for autophagic degradation. In the past few years it has been revealed that Atg8-interacting proteins include not only receptors but also components of the core autophagic machinery, proteins associated with vesicles and their transport, and specific proteins that are selectively degraded by autophagy. Atg8-interacting proteins contain a short linear LC3-interacting region/LC3 recognition sequence/Atg8-interacting motif (LIR/LRS/AIM) motif which is responsible for their interaction with Atg8-family proteins. These proteins are referred to as LIR-containing proteins (LIRCPs). So far, many experimental efforts have been carried out to identify new LIRCPs, leading to the characterization of some of them in the past 10 years. Given the need for the identification of LIRCPs in various organisms, we developed the iLIR database (https://ilir.warwick.ac.uk) as a freely available web resource, listing all the putative canonical LIRCPs identified in silico in the proteomes of 8 model organisms using the iLIR server, combined with a Gene Ontology (GO) term analysis. Additionally, a curated text-mining analysis of the literature permitted us to identify novel putative LICRPs in mammals that have not previously been associated with autophagy.     

Kinetic limitations during the simultaneous removal of <Emphasis Type="Italic">p</Emphasis>-cresol and sulfide in a denitrifying process

The aim of this study was to evaluate the capacity of a denitrifying consortium to achieve the simultaneous removal of nitrate, sulfide and p-cresol and elucidate the rate-limiting steps in the mixotrophic process. Nitrite reduction appeared as the most evident rate-limiting step in the denitrifying respiratory process. The nitrite reduction rate achieved was up to 57 times lower than the nitrate reduction rate during the simultaneous removal of sulfide and p-cresol. Negligible accumulation of N₂O occurred in the denitrifying cultures corroborating that nitrite reduction was the main rate-limiting step of the respiratory process. A synergistic effect of nitrate and sulfide is proposed to explain the accumulation of nitrite. The study also points at the oxidation of S⁰ as another rate-limiting step in the denitrifying process. Different respiratory rates were achieved with the distinct electron donors provided (p-cresol and sulfide). The oxidation rate of p-cresol (q_CRES) was generally higher (up to 2.6-fold in terms of reducing equivalents) than the sulfide oxidation rate (q_S2−), except for the experiments performed at 100 mg S²⁻ L⁻¹ in which q_S2− was slightly (~1.4-fold in terms of reducing equivalents) higher than q_CRES. The present study provides kinetic information, which should be considered when designing and operating denitrifying reactors to treat industrial wastewaters containing large amounts of sulfurous, nitrogenous and phenolic contaminants such as those generated from petrochemical refineries.