Bacterial protein meta-interactomes predict cross-species interactions and protein function

Background Protein-protein interactions (PPIs) can offer compelling evidence for protein function, especially when viewed in the context of proteome-wide interactomes. Bacteria have been popular subjects of interactome studies: more than six different bacterial species have been the subjects of comprehensive interactome studies while several more have had substantial segments of their proteomes screened for interactions. The protein interactomes of several bacterial species have been completed, including several from prominent human pathogens. The availability of interactome data has brought challenges, as these large data sets are difficult to compare across species, limiting their usefulness for broad studies of microbial genetics and evolution. Results In this study, we use more than 52,000 unique protein-protein interactions (PPIs) across 349 different bacterial species and strains to determine their conservation across data sets and taxonomic groups. When proteins are collapsed into orthologous groups (OGs) the resulting meta-interactome still includes more than 43,000 interactions, about 14,000 of which involve proteins of unknown function. While conserved interactions provide support for protein function in their respective species data, we found only 429 PPIs (~1% of the available data) conserved in two or more species, rendering any cross-species interactome comparison immediately useful. The meta-interactome serves as a model for predicting interactions, protein functions, and even full interactome sizes for species with limited to no experimentally observed PPI, including Bacillus subtilis and Salmonella enterica which are predicted to have up to 18,000 and 31,000 PPIs, respectively. Conclusions In the course of this work, we have assembled cross-species interactome comparisons that will allow interactomics researchers to anticipate the structures of yet-unexplored microbial interactomes and to focus on well-conserved yet uncharacterized interactors for further study. Such conserved interactions should provide evidence for important but yet-uncharacterized aspects of bacterial physiology and may provide targets for anti-microbial therapies

Pembagian Harta Warisan dalam Masyarakat Minangkabau di Kecamatan Medan Area Kelurahan Tegal Sari III Kota Medan

The change in the inheritance law of Minangkabau was identified by the agreement among ninik mamak (clan heads), cerdik pandai (the intellectuals), and generasi muda (the youth) in Bukittinggi in 1952. The agreement was strengthened by the seminar on the Minangkabau Customary Law in Padang in 1968. One of the clause was that joint property inherited by heirs had to comply with Faraid (religious obligation). The out-migrated Minangkabau community creates acculturation which influences their way of perception and thinking. Based on this background, the researcher studied the distribution of inheritance among the out-migrated Minangkabau community The Distribution of inheritance in the Minangkabau community at Kelurahan Tegal Sari III, Medan Area Subdistrict, Medan, is based on the Islamic Law. The factors of compliance and piety will cause customary law to be avoided. The change in heritance law can also accurs because of the factors of necessities of life

Isolation and expression studies of differentiation-specific genes in tobacco dihaploids using PCR-based subtractive hybridization method

The method of subtractive suppression hybridization has been used to detect and clone differentially expressed genes during differentiation. For this, we used dihaploid tobacco plants as starting material and compared mRNA from proliferating callus with that of differentiating callus. The dihaploid homozygous plants were chosen to get the expression of rare genes which are otherwise difficult to detect in diploid plants. The cDNAs after subtraction were cloned and a total of 41 unique clones were identified which are upregulated in differentiating tissue, among these 21 were novel while 20 showed homology with different genes in database. An explanation has been given regarding the role of these genes in the developmental process

Isolation of pollen early genes and analysis of expression pattern during the development of male gametophyte

The early events of pollen development are critical for the differentiation of male gametophyte. However, little is known about the molecular events that are unique to the early stages of pollen development. This study of gene expression during the pollen development is focused on identifying the early genes in Nicotiana tabacum anthers and characterizing the expression and regulation of these genes. A subtraction cDNA library was prepared from the early stages of pollen development (from dyad till uninucleate stage) and 113 unique genes differentially expressed were identified. Searches of the Nicotiana and other non-redundant database disclosed known or likely functions for 73 genes while 40 genes were of unknown function. Among those with unknown function 24 found matches in EST database while 16 showed 'no hit' or were novel. Northern blot analysis of 16 randomly picked clones as probes confirmed their expression in early stages of pollen development and no expression or lower expression in later stages. The tissue-specific expression studies showed that among these, 12 genes are anther-specific. To the best of our knowledge, these groups of clones represent the largest collection of 'early genes' isolated so far

New Insights into the Ligninolytic Capability of a Wood Decay Ascomycete▿

Wood-grown cultures of Daldinia concentrica oxidized a permethylated β-14C-labeled synthetic lignin to 14CO2 and also cleaved a permethylated α-13C-labeled synthetic lignin to give Cα-Cβ cleavage products that were detected by 13C nuclear magnetic resonance spectrometry. Therefore, this ascomycete resembles white-rot basidiomycetes in attacking the recalcitrant nonphenolic structures that predominate in lignin

Additional file 5: of Bacterial protein meta-interactomes predict cross-species interactions and protein function

Conserved interactors of unclear function. (XLS 29 kb

Additional file 6: of Bacterial protein meta-interactomes predict cross-species interactions and protein function

Contributions of individual bacterial taxons to the consensus meta-interactome. (XLS 42 kb