Comparative proteomic characteristic of Mycoplasmas (Mollycutes)

Saturating proteome identification and the study of post-translational protein modifications of Acholeplasma laidlawii using combination of single- and two-dimension gel electrophoresis followed by mass-spectrometry analysis have been carried out. Results were compared to the earlier identified proteome of Mycoplasma gallisepticum. It was found that M. gallisepticum and A. laidlawii express 61 and 58% of the annotated ORFs respectively. All subunits of DNA-polymerase III were identified during our study which indicates that our methods can detect single copies of a given protein per cell. Metabolic pathways of the respective mycoplasmas were compared further in this work.     

Most recent AluY insertions in human gene introns reduce the content of the primary transcripts in a cell type specific manner

Being the most effectively transposed primate-specific SINEs, Alu elements are present in more than one million copies in the human genome and include most recently transposed subsets of AluY elements that are polymorphic in humans. Although Alu elements are commonly thought to play an essential role in shaping and functioning of primate genomes, the understanding of the impact of recent Alu insertions on human gene expression is far from being comprehensive. Here we compared hnRNA contents for allele pairs of genes heterozygous for AluY insertions in their introns in human cell lines of various origins. We demonstrated that some AluY insertions correlated with decreased content of the corresponding hnRNAs. The effect observed does not depend on sequences of Alu elements and their orientation but is likely to be cell type specific.     

Proteomic response of bacteria during the interaction with a host cell in a model of <Emphasis Type="Italic">Mycoplasma gallisepticum</Emphasis>

Parasitism, which is a way of the coexistence of bacteria with a host, is a very interesting phenomenon. Although the pathogenicity of many microorganisms has been studied in detail, many aspects of this phenomenon remain poorly understood for most bacteria. Among interesting objects for studying pathogen–host interactions are the members of the Mycoplasma genus. Despite a very broad geographical range of habitat of these bacteria, their pathogenicity has been poorly studied. Almost all living beings are the hosts of mycoplasmas, and the reduced genome of these microorganisms makes them a convenient object for model studies. Here, we have described for the first time an experimental label-free method for the analysis of the protein profile of a bacterium immediately during its interaction with a host cell, which made it possible to understand what changes the pathogen undergoes at this stage of infection. The method involves the sampling of eukaryotic cells at different times of cultivation with the pathogen, the sedimentation of infected cells, the preparation of a cell lysate, the hydrolytic cleavage of cell proteins, and their identification by mass spectrometry (HPLC–MS). Changes in the protein abundance were analyzed by the method of multiple reaction monitoring (MRM). In the present work, a model of the interaction of the bacterium Mycoplasma gallisepticum with chicken erythroblasts (HD3 cells) at the stage of acute infection was studied. A panel of 100 proteins was taken for the analysis, which were chosen based on their functions and literature data. To obtain the greatest number of identified proteins, several methods of their hydrolytic cleavage with subsequent preparation of the peptide extract were used: digestion in solution using the RapiGest SF surfactant, digestion using sodium deoxycholate and urea, and the digestion of proteins in gel. As a result, proteins were identified that, probably, are involved in the interaction of M. gallisepticum with the host cell at early infection stages; most of them were the proteins of adhesion, glycolysis, and ribosomal proteins.     

A new database on polymorphic retroelements in human genome (PRED)

Comparison of primate genomes sequences has confirmed the evidence that substantial part of intra- and interspecies differences is provided by retroelements. Human genome contains thousands of polymorphic retroelement copies considered to be perspective molecular genetic markers of new generation. However utilization of polymorphic retroelements as molecular genetic markers is limited due to lack of systematic data on their number, genomic context and distribution among human populations. We have created first bilingual (Russian/English) internet-resource devoted to known polymorphic retroelements discovered in human genome by our group as well as by other researchers worldwide. The database contains information about each retroelement copy location, position relative to known and predicted genes, frequency of alleles in human populations and others. Our internet portal allows to perform a search in database using multiple search conditions and available on http://labcfg.ibch.ru/home.html. The database provides an opportunity to investigate distribution of polymorphic retroelements in human genome and to design new genetic markers for various population and medical studies.     

Proteome of HU-Lacking E. coli Studied by Means of 2D Gel Electrophoresis

Russian Journal of Bioorganic Chemistry - Histone-like protein HU is a dimeric nucleoid-associated protein (NAP). HU is the most conserved NAP. It binds nonspecifically to duplex DNA with a...     

A new polymorphic retroelement database (PRED) for the human genome

Comparison of primate genomic sequences has demonstrated that the intra-and interspecific genetic variation is provided by retroelements (REs). The human genome contains many thousands of polymorphic RE copies, which are regarded as a promising source of new generation molecular genetic markers. However, the absence of systematized data on the RE number, distribution, genomic context, and abundance in various human populations limits the use of RE insertion polymorphism. We designed the first bilingual (Russian/English) web resource on the known polymorphic REs discovered both by our team and other researchers. The database contains the information about the genomic location of each RE, its position relative to known and predicted genes, abundance in human populations, and other data. Our web portal () allows a search of the database with user-specified parameters. The database makes it possible to most comprehensively analyze the RE distribution in the human genome and to design molecular genetic markers for studies of human genome diversity and biomedical applications.     

Comparative proteomic characteristic of mycoplasmas (Mollicutes)

Using one- and two-dimensional gel electrophoresis, various types of mass-spectrometry, and combinations of these two methods, saturating identification of mycoplasm Acholeplasma laidlawii proteome and study of proteins carrying posttranslational modifications were performed. We compared our data with earlier identified proteome of Mycoplasma gallisepticum. It was shown that M. gallisepticum and A. laidlawii expressed 61 and 58% of the proteins of the annotated open reading frames, respectively. All subunits of DNA-polymerase III were identified for A. laidlawii during our study, which indicates that our techniques enable detection of single copies of mollicutes proteins per cell. Metabolic pathways of respective mycoplasmas is compared in this research.