In rice (Oryza sativa), the presence of a dominant Badh2 allele encoding betaine aldehyde dehydrogenase (BADH2) inhibits the synthesis of 2-acetyl-1-pyrroline (2AP), a potent flavor component in rice fragrance. By contrast, its two recessive alleles, badh2-E2 and badh2-E7, induce 2AP formation. Badh2 was found to be transcribed in all tissues tested except for roots, and the transcript was detected at higher abundance in young, healthy leaves than in other tissues. Multiple Badh2 transcript lengths were detected, and the complete, full-length Badh2 transcript was much less abundant than partial Badh2 transcripts. 2AP levels were significantly reduced in cauliflower mosaic virus 35S-driven transgenic lines expressing the complete, but not the partial, Badh2 coding sequences. In accordance, the intact, full-length BADH2 protein (503 residues) appeared exclusively in nonfragrant transgenic lines and rice varieties. These results indicate that the full-length BADH2 protein encoded by Badh2 renders rice nonfragrant by inhibiting 2AP biosynthesis. The BADH2 enzyme was predicted to contain three domains: NAD binding, substrate binding, and oligomerization domains. BADH2 was distributed throughout the cytoplasm, where it is predicted to catalyze the oxidization of betaine aldehyde, 4-aminobutyraldehyde (AB-ald), and 3-aminopropionaldehyde. The presence of null badh2 alleles resulted in AB-ald accumulation and enhanced 2AP biosynthesis. In summary, these data support the hypothesis that BADH2 inhibits 2AP biosynthesis by exhausting AB-ald, a presumed 2AP precursor.

As one of the most important reversible protein post-translation modifications, ubiquitination has been reported to be involved in lots of biological processes and closely implicated with various diseases. To fully decipher the molecular mechanisms of ubiquitination-related biological processes, an initial but crucial step is the recognition of ubiquitylated substrates and the corresponding ubiquitination sites. Here, a new bioinformatics tool named CKSAAP_UbSite was developed to predict ubiquitination sites from protein sequences. With the assistance of Support Vector Machine (SVM), the highlight of CKSAAP_UbSite is to employ the composition of k-spaced amino acid pairs surrounding a query site (i.e. any lysine in a query sequence) as input. When trained and tested in the dataset of yeast ubiquitination sites (Radivojac et al, Proteins, 2010, 78: 365–380), a 100-fold cross-validation on a 1∶1 ratio of positive and negative samples revealed that the accuracy and MCC of CKSAAP_UbSite reached 73.40% and 0.4694, respectively. The proposed CKSAAP_UbSite has also been intensively benchmarked to exhibit better performance than some existing predictors, suggesting that it can be served as a useful tool to the community. Currently, CKSAAP_UbSite is freely accessible at http://protein.cau.edu.cn/cksaap_ubsite/. Moreover, we also found that the sequence patterns around ubiquitination sites are not conserved across different species. To ensure a reasonable prediction performance, the application of the current CKSAAP_UbSite should be limited to the proteome of yeast.

Rice blast caused by Magnaporthe oryzae is one of the most destructive diseases of rice worldwide. The fungal pathogen is notorious for its ability to overcome host resistance. To better understand its genetic variation in nature, we sequenced the genomes of two field isolates, Y34 and P131. In comparison with the previously sequenced laboratory strain 70-15, both field isolates had a similar genome size but slightly more genes. Sequences from the field isolates were used to improve genome assembly and gene prediction of 70-15. Although the overall genome structure is similar, a number of gene families that are likely involved in plant-fungal interactions are expanded in the field isolates. Genome-wide analysis on asynonymous to synonymous nucleotide substitution rates revealed that many infection-related genes underwent diversifying selection. The field isolates also have hundreds of isolate-specific genes and a number of isolate-specific gene duplication events. Functional characterization of randomly selected isolate-specific genes revealed that they play diverse roles, some of which affect virulence. Furthermore, each genome contains thousands of loci of transposon-like elements, but less than 30% of them are conserved among different isolates, suggesting active transposition events in M. oryzae. A total of approximately 200 genes were disrupted in these three strains by transposable elements. Interestingly, transposon-like elements tend to be associated with isolate-specific or duplicated sequences. Overall, our results indicate that gain or loss of unique genes, DNA duplication, gene family expansion, and frequent translocation of transposon-like elements are important factors in genome variation of the rice blast fungus. Magnaporthe oryzae is the causal agent of rice blast that is mainly controlled with resistance cultivars. However, genetic variations in the pathogen often lead to overcoming R gene-mediated resistance in rice cultivars. In this study we sequenced two field isolates from China and Japan. In comparison with the laboratory strain that was previously sequenced, the field isolates have a similar genome size and overall genome structure. However, they have slightly more genes and contain a number of expanded gene families that are likely involved in plant-fungal interactions. Each of the isolates has specific genes, some of which affect virulence and some others are important for asexual development. The three strains differ noticeably in the distribution of transposon-like elements. Many of the transposable elements tend to be associated with isolate-specific or duplicated sequences. This study revealed genetic factors involved in genome variation of the rice blast fungus.

The identification of human-virus protein-protein interactions (PPIs) is an essential and challenging research topic, potentially providing a mechanistic understanding of viral infection. Given that the experimental determination of human-virus PPIs is time-consuming and labor-intensive, computational methods are playing an important role in providing testable hypotheses, complementing the determination of large-scale interactome between species. In this work, we applied an unsupervised sequence embedding technique (doc2vec) to represent protein sequences as rich feature vectors of low dimensionality. Training a Random Forest (RF) classifier through a training dataset that covers known PPIs between human and all viruses, we obtained excellent predictive accuracy outperforming various combinations of machine learning algorithms and commonly-used sequence encoding schemes. Rigorous comparison with three existing human-virus PPI prediction methods, our proposed computational framework further provided very competitive and promising performance, suggesting that the doc2vec encoding scheme effectively captures context information of protein sequences, pertaining to corresponding protein-protein interactions. Our approach is freely accessible through our web server as part of our host-pathogen PPI prediction platform (http://zzdlab.com/InterSPPI/). Taken together, we hope the current work not only contributes a useful predictor to accelerate the exploration of human-virus PPIs, but also provides some meaningful insights into human-virus relationships.

Bifidobacteria, one of the relatively dominant components of the human intestinal microbiota, are considered one of the key groups of beneficial intestinal bacteria (probiotic bacteria). However, in addition to health-promoting taxa, the genus Bifidobacterium also includes Bifidobacterium dentium, an opportunistic cariogenic pathogen. The genetic basis for the ability of B. dentium to survive in the oral cavity and contribute to caries development is not understood. The genome of B. dentium Bd1, a strain isolated from dental caries, was sequenced to completion to uncover a single circular 2,636,368 base pair chromosome with 2,143 predicted open reading frames. Annotation of the genome sequence revealed multiple ways in which B. dentium has adapted to the oral environment through specialized nutrient acquisition, defences against antimicrobials, and gene products that increase fitness and competitiveness within the oral niche. B. dentium Bd1 was shown to metabolize a wide variety of carbohydrates, consistent with genome-based predictions, while colonization and persistence factors implicated in tissue adhesion, acid tolerance, and the metabolism of human saliva-derived compounds were also identified. Global transcriptome analysis demonstrated that many of the genes encoding these predicted traits are highly expressed under relevant physiological conditions. This is the first report to identify, through various genomic approaches, specific genetic adaptations of a Bifidobacterium taxon, Bifidobacterium dentium Bd1, to a lifestyle as a cariogenic microorganism in the oral cavity. In silico analysis and comparative genomic hybridization experiments clearly reveal a high level of genome conservation among various B. dentium strains. The data indicate that the genome of this opportunistic cariogen has evolved through a very limited number of horizontal gene acquisition events, highlighting the narrow boundaries that separate commensals from opportunistic pathogens. The accessibility of complete bacterial genome sequences has provided important changes to the field of microbiology by significantly enhancing our understanding of the physiology, genetics, and evolutionary development of bacteria. Bifidobacteria are among such microorganisms, being mammalian commensals of biotechnological significance due to their perceived role in maintaining a balanced gastrointestinal (GIT) microflora. Bifidobacteria are therefore often applied as health-promoting or probiotic components in functional food products and represent a growing area of scientific interest. However, within the genus Bifidobacterium not all species provide beneficial effects on the host's health. In fact, the Bifidobacterium dentium species is considered an opportunistic pathogen since it has been associated with the development of dental caries. In this manuscript, we describe the complete genetic make-up of the B. dentium Bd1 genome and discuss functions that explain how this microorganism has adapted to the oral human cavity and imparts a cariogeneous phenotype. Moreover, we performed comparative genomic analyses of B. dentium genome with other bifidobacterial genomes in order to trace genetic differences/similarities between the opportunistic oral pathogen B. dentium Bd1 and closely related intestinal bifidobacteria.