Distribution of Hepatitis B Genotypes Among Hepatitis B Patients Visiting Decode Genomics Research Center

The hepatitis B virus (HBV) is non-cytopathic, hepatotropic and enveloped virus which causes Hepatitis B and infects the liver causing inflammation and hepatocellular necrosis. The genome sequence database shows that HBV has ten genetic diversities (A-J) ten in which the HBV genotypes, I and J are the new one. Three major genotypes of HBV (A, C and D) were found in Nepal. Despite being a low prevalence, Nepal has a diversity of hepatitis B. Hence, the study aims to determine the distribution of hepatitis B genotypes among the hepatitis B patients visiting Decode Genomics Research Center. HBV genotypes were determined by using a simpler, more rapid, and more specific genotyping system for HBV involving PCR using type-specific primers. Our study showed that different HBV genotypes were identified in which genotype D to be predominant one followed by C and also showed presence of genotype A, B and F. Many recombinant genotypes were also present in our study.

Comparative genomics and metabolomics analysis of Riemerella anatipestifer strain CH-1 and CH-2

Riemerella anatipestifer is a major pathogenic microorganism in poultry causing serositis with significant mortality. Serotype 1 and 2 were most pathogenic, prevalent, and liable over the world. In this study, the intracellular metabolites in R. anatipestifer strains RA-CH-1 (serotype 1) and RA-CH-2 (serotype 2) were identified by gas chromatography-mass spectrometer (GC–MS). The metabolic profiles were performed using hierarchical clustering and partial least squares discriminant analysis (PLS-DA). The results of hierarchical cluster analysis showed that the amounts of the detected metabolites were more abundant in RA-CH-2. RA-CH-1 and RA-CH-2 were separated by the PLS-DA model. 24 potential biomarkers participated in nine metabolisms were contributed predominantly to the separation. Based on the complete genome sequence database and metabolite data, the first large-scale metabolic models of iJL463 (RA-CH-1) and iDZ470 (RA-CH-2) were reconstructed. In addition, we explained the change of purine metabolism combined with the transcriptome and metabolomics data. The study showed that it is possible to detect and differentiate between these two organisms based on their intracellular metabolites using GC–MS. The present research fills a gap in the metabolomics characteristics of R. anatipestifer.

Identification of MMP-like protein from Streptococcus mitis

Streptococcus mitis is a normal commensal of the human oral cavity and oropharynx. This microorganism is an opportunistic pathogen in immune compromised hosts and a cause of invasive diseases such as infective endocarditis. We isolated a matrix metalloprotease (MMP)-like protein of S. mitis. The gene for the MMP-like protein was found on the genome sequence database of S. mitis . The gene encodes a protein consisting of 240 amino acid residues with a conserved zinc-binding motif (HEXXHXXGXXH) among the matrix metallopeptidase family. The gene was PCR-amplified from S. mitis ATCC 49456 and cloned for construction of the recombinant protein. The recombinant MMP-like protein with a GST-tag was purified and the enzymatic activity was assessed. The recombinant protein showed approximately half the level of MMP-like activity as compared to human recombinant MMP-8. The MMP-like protein of S. mitis may be involved in the pathogenesis of infection to the dentin with collagen fibers and systemic invasive diseases.

Genome Sequence Resource of “Candidatus Liberibacter asiaticus” strain Myan16 from Myanmar

“Candidatus Liberibacter asiaticus” (CaLas), an uncultured α-proteobacterium, is associated with citrus Huanglongbing (HLB, yellow shoot disease), a destructive disease threatening citrus production worldwide. Here, we reported the draft genome sequence of CaLas strain Myan16 from a HLB-affected lime tree in Myitkyina, Kachin State, Myanmar. The strain Myan16 genome is 1,229,102 bp with an average G+C content of 36.4%, along with a circular prophage: P-Myan16-2 (36,303 bp, Type 2). This is the first genome sequence of CaLas strain from Myanmar, which will enrich the current CaLas genome sequence database and facilitate HLB epidemiology research in Asia and world.

Variation in Seed Metabolites between Two Indica Rice Accessions Differing in Seed Longevity

For a better understanding of germination after seed storage, metabolite profiling was conducted using hybrid triple quadrupole time-of-flight (QTOF) mass spectrometry. After moisture content (MC) equilibration, seeds of “WAS170” (short-lived) and “IR65483” (long-lived) were stored at 10.9% MC and 45 °C. Samples for metabolite analysis were taken after 0 and 20 days of storage. Among 288 metabolites, two flavonoids (kaempferide and quercetin-3-arabinoside), one amino acid (S-sulfocysteine) and one sugar (D-glucose) increased in “IR65483” seeds after storage but were not detected in “WAS170” seeds. Based on the genome sequence database, we identified clear allelic differences with non-synonymous mutations on the six flavonol synthase genes regulating the accumulation of kaempferol- and quercetin-metabolites. On the other hand, two metabolites (thiamine monophosphate and harmaline) increased in short-lived seeds after storage; these metabolites could be potential biochemical indicators of seed deterioration.

Cross-species transmission and differential fate of an endogenous retrovirus in three mammal lineages

Endogenous retroviruses (ERVs) arise from retroviruses chromosomally integrated in the host germline. ERVs are common in vertebrate genomes and provide a valuable fossil record of past retroviral infections to investigate the biology and evolution of retroviruses over a deep time scale, including cross-species transmission events. Here we took advantage of a catalog of ERVs we recently produced for the bat Myotis lucifugus to seek evidence for infiltration of these retroviruses in other mammalian species (>100) currently represented in the genome sequence database. We provide multiple lines of evidence for the cross-ordinal transmission of a gammaretrovirus endogenized independently in the lineages of vespertilionid bats, felid cats and pangolin ~13-25 million years ago. Following its initial introduction, the ERV amplified extensively in parallel in both bat and cat lineages, generating hundreds of species-specific insertions throughout evolution. However, despite being derived from the same viral species, phylogenetic and selection analyses suggest that the ERV experienced different amplification dynamics in the two mammalian lineages. In the cat lineage, the ERV appears to have expanded primarily by retrotransposition of a single proviral progenitor that lost infectious capacity shortly after endogenization. In the bat lineage, the ERV followed a more complex path of germline invasion characterized by both retrotransposition and multiple infection events. The results also suggest that some of the bat ERVs have maintained infectious capacity for extended period of time and may be still infectious today. This study provides one of the most rigorously documented cases of cross-ordinal transmission of a mammalian retrovirus. It also illustrates how the same retrovirus species has transitioned multiple times from an infectious pathogen to a genomic parasite (i.e. retrotransposon), yet experiencing different invasion dynamics in different mammalian hosts.

The Succinate Dehydrogenase Genes of the Silkworm, Bombyx mori

The succinate sehydrogenase (SDH) encoded by nuclear genome is a conjugating enzyme in the inner mitochondrial membrane. It is a junction for oxidative phosphorylation and the electron transport chain.As a part of complex II on the inner mt membranes, the SDH consists of four subunit proteins (A to D). We searched the genome sequence database of Bombyx mori with the Drosophila melanogaste and Nasonia vitripennis SDH by tBlastn and determined the structure of all putative B. mori genes of sdh by DNAMAN. The main results are as follows: The SdhAgene of B. mori contains 13 exons. The lengths of its cDNA is 2 880 bp at least. The SdhB gene of B. mori contains 1 exon only. The lengths of cDNA is 2 847 bp at least. The SdhC gene contains 4 exons. The lengths of cDNA is 714 bp at least. The SdhD gene contains 4 exons, too. The lenghts of cDNA is 1 976 bp at least.

Discovery of a Novel Styrene Monooxygenase Originating from the Metagenome

ABSTRACT Oxygenases form an interesting class of biocatalysts, as they typically perform oxygenations with exquisite chemo-, regio-, and/or enantioselectivity. It has been observed that, once heterologously expressed in Escherichia coli, some oxygenases are able to form the blue pigment indigo. We have exploited this characteristic to screen a metagenomic library derived from loam soil and identified a novel oxygenase. This oxygenase shows 50% sequence identity with styrene monooxygenases from pseudomonads (StyA). Only a limited number of homologs can be found in the genome sequence database, indicating that this biocatalyst is a member of a relatively small family of bacterial monooxygenases. The newly identified monooxygenase catalyzes the epoxidation of styrene and styrene derivatives and forms the corresponding (S)-epoxides with excellent enantiomeric excess [e.g., (S)-styrene oxide is formed with >99% enantiomeric excess, ee] and therefore is named styrene monooxgenase subunit A (SmoA). SmoA shows high enantioselectivity towards aromatic sulfides [e.g., (R)-ethyl phenyl sulfoxide is formed with 92% ee]. This excellent enantioselectivity in combination with the moderate sequence identity forms a clear indication that SmoA from a metagenomic origin represents a new enzyme within the small family of styrene monooxygenases.