Revision of the Capsaspora genome using read mating information adjusts the view on premetazoan genome

The genome sequences of unicellular holozoans, the closest relatives to animals, are shedding light on the evolution of animal multicellularity, shaping the genetic contents of the putative premetazoans. However, the assembly quality of the genomes remains poor compared to the major model organisms such as human and fly. Improving the assembly is critical for precise comparative genomics studies and further molecular biological studies requiring accurate sequence information such as enhancer analysis and genome editing. In this report, we present a new strategy to improve the assembly by fully exploiting the information of Illumina mate-pair reads. By visualizing the distance and orientation of the mapped read pairs, we could highlight the regions where possible assembly errors exist in the genome sequence of Capsaspora, a lineage of unicellular holozoans. Manual modification of these errors repaired 590 assembly problems in total and reassembled 84 supercontigs into 55. Our telomere prediction analysis using the read pairs containing the pan-eukaryotic telomere-like sequence identified at least 13 chromosomes. The resulting new assembly posed us a re-annotation of 112 genes, including 15 putative receptor protein tyrosine kinases. Our strategy thus provides a useful approach for improving assemblies of draft genomes, and the new Capsaspora genome offers us an opportunity to adjust the view on the genome of the unicellular animal ancestor.     

Origin and development of oligoadenylate synthetase immune system

Background

Oligoadenylate synthetases (OASs) are widely distributed in Metazoa including sponges, fish, reptiles, birds and mammals and show large variation, with one to twelve members in any given species. Upon double-stranded RNA (dsRNA) binding, avian and mammalian OASs generate the second messenger 2'-5'-linked oligoadenylate (2-5A), which activates ribonuclease L (RNaseL) and blocks viral replication. However, how Metazoa shape their OAS repertoires to keep evolutionary balance to virus infection is largely unknown. We performed comprehensive phylogenetic and functional analyses of OAS genes from evolutionarily lower to higher Metazoa to demonstrate how the OAS repertoires have developed anti-viral activity and diversified their functions.

Results

Ancient Metazoa harbor OAS genes, but lack both upstream and downstream genes of the OAS-related pathways, indicating that ancient OASs are not interferon-induced genes involved in the innate immune system. Compared to OASs of ancient Metazoa (i.e. sponge), the corresponding ones of higher Metazoa present an increasing number of basic residues on the OAS/dsRNA interaction interface. Such an increase of basic residues might improve their binding affinity to dsRNA. Moreover, mutations of functional residues in the active pocket might lead to the fact that higher Metazoan OASs lose the ability to produce 3'-5'-linked oligoadenylate (3-5A) and turn into specific 2-5A synthetases. In addition, we found that multiple rounds of gene duplication and domain coupling events occurred in the OAS family and mutations at functionally critical sites were observed in most new OAS members.

Conclusions

We propose a model for the expansion of OAS members and provide comprehensive evidence of subsequent neo-functionalization and sub-functionalization. Our observations lay the foundation for interrogating the evolutionary transition of ancient OAS genes to host defense genes and provide important information for exploring the unknown function of the OAS gene family.

     

Association Analysis of Genetic Variants in the Myosin IXB Gene in Acute Pancreatitis

Introduction

Impairment of the mucosal barrier plays an important role in the pathophysiology of acute pancreatitis. The myosin IXB (MYO9B) gene and the two tight-junction adaptor genes, PARD3 and MAGI2, have been linked to gastrointestinal permeability. Common variants of these genes are associated with celiac disease and inflammatory bowel disease, two other conditions in which intestinal permeability plays a role. We investigated genetic variation in MYO9B, PARD3 and MAGI2 for association with acute pancreatitis.

Methods

Five single nucleotide polymorphisms (SNPs) in MYO9B, two SNPs in PARD3, and three SNPs in MAGI2 were studied in a Dutch cohort of 387 patients with acute pancreatitis and over 800 controls, and in a German cohort of 235 patients and 250 controls.

Results

Association to MYO9B and PARD3 was observed in the Dutch cohort, but only one SNP in MYO9B and one in MAGI2 showed association in the German cohort (p < 0.05). Joint analysis of the combined cohorts showed that, after correcting for multiple testing, only two SNPs in MYO9B remained associated (rs7259292, p = 0.0031, odds ratio (OR) 1.94, 95% confidence interval (95% CI) 1.35-2.78; rs1545620, p = 0.0006, OR 1.33, 95% CI 1.16-1.53). SNP rs1545620 is a non-synonymous SNP previously suspected to impact on ulcerative colitis. None of the SNPs showed association to disease severity or etiology.

Conclusion

Variants in MYO9B may be involved in acute pancreatitis, but we found no evidence for involvement of PARD3 or MAGI2.     

Periodic Gene Expression Patterns during the Highly Synchronized Cell Nucleus and Organelle Division Cycles in the Unicellular Red Alga Cyanidioschyzon merolae

Previous cell cycle studies have been based on cell-nuclearproliferation only. Eukaryotic cells, however, have double membranes-boundorganelles, such as the cell nucleus, mitochondrion, plastidsand single-membrane-bound organelles such as ER, the Golgi body,vacuoles (lysosomes) and microbodies. Organelle proliferations,which are very important for cell functions, are poorly understood.To clarify this, we performed a microarray analysis during thecell cycle of Cyanidioschyzon merolae. C. merolae cells containa minimum set of organelles that divide synchronously. The nuclear,mitochondrial and plastid genomes were completely sequenced.The results showed that, of 158 genes induced during the S orG2-M phase, 93 were known and contained genes related to mitochondrialdivision, ftsZ1-1, ftsz1-2 and mda1, and plastid division, ftsZ2-1,ftsZ2-2 and cmdnm2. Moreover, three genes, involved in vesicletrafficking between the single-membrane organelles such as vps29and the Rab family protein, were identified and might be relatedto partitioning of single-membrane-bound organelles. In othergenes, 46 were hypothetical and 19 were hypothetical conserved.The possibility of finding novel organelle division genes fromhypothetical and hypothetical conserved genes in the S and G2-Mexpression groups is discussed.     

Mutant genes at the r and rb loci affect the structure and physico-chemical properties of pea seed starches

Mutant genes at two loci, r and rb, known to encode genes affectingthe starch biosynthetic pathway, were studied for their effecton the structure and gelatinization of pea seed starches. Comparisonswere made using starches from four lines {RRRbRb, rrRbRb, RRrbrb,and rrrbrb), near-isogenic except for genes at these two loci.All the starches had C-type X-ray diffraction patterns, butdifferent contents of ‘A’ and ‘B’ polymorphs.The presence of a mutation at either locus increased the ‘B’polymorph content in the starches, although the influence ofthe r mutation was much greater than that of rb. Differenceswere discovered in the crystalline stucture of the rrRbRb starchwhich correlated with a high content of amorphous phase as wellas with the changes in amylopectin structure. In addition, changesin the crystalline structure of this sample correlated witha lack of co-operative transition during starch gelatinizationin excess water. The RRrbrb starch had a greatly increased enthalpyof gelatinization in excess water compared with the wild-typestarch. It is proposed that this effect is connected with specificcharge interactions between the molecules in the starch granule.The rrrbrb starch had parameters of crystalline structure andgelatinization which reflected the different influences of thetwo genes. With regard to gelatinization, this starch had relativelywide co-operative transition and low enthalpy and a very highpeak temperature of transition. Key words: Pisum sativum, starch structure, genetic effects, rugosus mutants     

Synergistic Function of rolB, rolC, ORF13 and ORF14 of TL-DNA of Agrobacterium rhizogenes in Hairy Root Induction in Nicotiana tabacum

Comparison of the frequency of rooting in the tobacco leaf segmentsinoculated with Agrobacterium tumefaciens harboring variouscombinations of rolB, rolC, ORF13 and ORF14 of TL-DNA of Riplasmid (pRiHRI) revealed that the genes differ in their functionto stimulate adventitious root induction. A single gene rolBinduced roots, while rolC, ORF13 and ORF14 independently promotedthe root induction by the rolB gene. The effects of these geneson the rolB-mediated rooting were in the order of ORF13>rolCORF14. Present address: Laboratory of Phylogenetic Botany, Departmentof Biology, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba,263-8522 Japan. ² Present address: Department of Chemical and Biological Sciences,Faculty of Science, Japan Women's University, 2-8-1 Mejirodai,Bunkyo-ku, Tokyo, 112-8681 Japan.