Professional Education

  • Doctor of Philosophy, University of Wyoming (2013)
  • Diploma, Novosibirsk State University (2007)

Stanford Advisors

All Publications

  • Proteins Related to the Type I Secretion System Are Associated with Secondary SecA_DEAD Domain Proteins in Some Species of Planctomycetes, Verrucomicrobia, Proteobacteria, Nitrospirae and Chlorobi PLOS ONE Kamneva, O. K., Poudel, S., Ward, N. L. 2015; 10 (6)


    A number of bacteria belonging to the PVC (Planctomycetes-Verrucomicrobia-Chlamydiae) super-phylum contain unusual ribosome-bearing intracellular membranes. The evolutionary origins and functions of these membranes are unknown. Some proteins putatively associated with the presence of intracellular membranes in PVC bacteria contain signal peptides. Signal peptides mark proteins for translocation across the cytoplasmic membrane in prokaryotes, and the membrane of the endoplasmic reticulum in eukaryotes, by highly conserved Sec machinery. This suggests that proteins might be targeted to intracellular membranes in PVC bacteria via the Sec pathway. Here, we show that canonical signal peptides are significantly over-represented in proteins preferentially present in PVC bacteria possessing intracellular membranes, indicating involvement of Sec translocase in their cellular targeting. We also characterized Sec proteins using comparative genomics approaches, focusing on the PVC super-phylum. While we were unable to detect unique changes in Sec proteins conserved among membrane-bearing PVC species, we identified (1) SecA ATPase domain re-arrangements in some Planctomycetes, and (2) secondary SecA_DEAD domain proteins in the genomes of some Planctomycetes, Verrucomicrobia, Proteobacteria, Nitrospirae and Chlorobi. This is the first report of potentially duplicated SecA in Gram-negative bacteria. The phylogenetic distribution of secondary SecA_DEAD domain proteins suggests that the presence of these proteins is not related to the occurrence of PVC endomembranes. Further genomic analysis showed that secondary SecA_DEAD domain proteins are located within genomic neighborhoods that also encode three proteins possessing domains specific for the Type I secretion system.

    View details for DOI 10.1371/journal.pone.0129066

    View details for Web of Science ID 000356630900207

    View details for PubMedID 26030905

  • Reconciliation Approaches to Determining HGT, Duplications, and Losses in Gene Trees NEW APPROACHES TO PROKARYOTIC SYSTEMATICS Kamneva, O. K., Ward, N. L. 2014; 41: 183-199
  • Genomics and Bioinformatics of the PVC Superphylum Planctomycetes: Cell Structure, Origins and Biology Kamneva, O. K., Haft, D. H., Knight, S. J., Liberles, D. A., Ward, N. L. Humana Press. 2013: 165-193
  • Analysis of Genome Content Evolution in PVC Bacterial Super-Phylum: Assessment of Candidate Genes Associated with Cellular Organization and Lifestyle GENOME BIOLOGY AND EVOLUTION Kamneva, O. K., Knight, S. J., Liberles, D. A., Ward, N. L. 2012; 4 (12): 1375-1390


    The Planctomycetes, Verrucomicrobia, Chlamydiae (PVC) super-phylum contains bacteria with either complex cellular organization or simple cell structure; it also includes organisms of different lifestyles (pathogens, mutualists, commensal, and free-living). Genome content evolution of this group has not been studied in a systematic fashion, which would reveal genes underlying the emergence of PVC-specific phenotypes. Here, we analyzed the evolutionary dynamics of 26 PVC genomes and several outgroup species. We inferred HGT, duplications, and losses by reconciliation of 27,123 gene trees with the species phylogeny. We showed that genome expansion and contraction have driven evolution within Planctomycetes and Chlamydiae, respectively, and balanced each other in Verrucomicrobia and Lentisphaerae. We also found that for a large number of genes in PVC genomes the most similar sequences are present in Acidobacteria, suggesting past and/or current ecological interaction between organisms from these groups. We also found evidence of shared ancestry between carbohydrate degradation genes in the mucin-degrading human intestinal commensal Akkermansia muciniphila and sequences from Acidobacteria and Bacteroidetes, suggesting that glycoside hydrolases are transferred laterally between gut microbes and that the process of carbohydrate degradation is crucial for microbial survival within the human digestive system. Further, we identified a highly conserved genetic module preferentially present in compartmentalized PVC species and possibly associated with the complex cell plan in these organisms. This conserved machinery is likely to be membrane targeted and involved in electron transport, although its exact function is unknown. These genes represent good candidates for future functional studies.

    View details for DOI 10.1093/gbe/evs113

    View details for Web of Science ID 000313215900019

    View details for PubMedID 23221607

  • Two promoters and two translation start sites control the expression of the Shigella flexneri outer membrane protease IcsP ARCHIVES OF MICROBIOLOGY Hensley, C. T., Kamneva, O. K., Levy, K. M., Labahn, S. K., Africa, L. A., Wing, H. J. 2011; 193 (4): 263-274


    The Shigella flexneri outer membrane protease IcsP proteolytically cleaves the actin-based motility protein IcsA from the bacterial surface. The icsP gene is monocistronic and lies downstream of an unusually large intergenic region on the Shigella virulence plasmid. In silico analysis of this region predicts a second transcription start site 84 bp upstream of the first. Primer extension analyses and beta-galactosidase assays demonstrate that both transcription start sites are used. Both promoters are regulated by the Shigella virulence gene regulator VirB and both respond similarly to conditions known to influence Shigella virulence gene expression (iron concentration, pH, osmotic pressure, and phase of growth). The newly identified promoter lies upstream of a Shine-Dalgarno sequence and second 5'-ATG-3', which is in frame with the annotated icsP gene. The use of either translation start site leads to the production of IcsP capable of proteolytically cleaving IcsA. A bioinformatic scan of the Shigella genome reveals multiple occurrences of in-frame translation start sites associated with putative Shine-Dalgarno sequences, immediately upstream and downstream of annotated open reading frames. Taken together, our observations support the possibility that the use of in-frame translation start sites may generate different protein isoforms, thereby expanding the proteome encoded by bacterial genomes.

    View details for DOI 10.1007/s00203-010-0669-2

    View details for Web of Science ID 000289443200004

    View details for PubMedID 21225241

  • Genomic and experimental evidence suggests that Verrucomicrobium spinosum interacts with eukaryotes FRONTIERS IN MICROBIOLOGY Sait, M., Kamneva, O. K., Fay, D. S., Kirienko, N. V., Polek, J., Shirasu-Hiza, M. M., Ward, N. L. 2011; 2
  • Myosin Cross-reactive Antigen of Streptococcus pyogenes M49 Encodes a Fatty Acid Double Bond Hydratase That Plays a Role in Oleic Acid Detoxification and Bacterial Virulence JOURNAL OF BIOLOGICAL CHEMISTRY Volkov, A., Liavonchanka, A., Kamneva, O., Fiedler, T., Goebel, C., Kreikemeyer, B., Feussner, I. 2010; 285 (14): 10353-10361


    The myosin cross-reactive antigen (MCRA) protein family is highly conserved among different bacterial species ranging from Gram-positive to Gram-negative bacteria. Besides their ubiquitous occurrence, knowledge about the biochemical and physiological function of MCRA proteins is scarce. Here, we show that MCRA protein from Streptococcus pyogenes M49 is a FAD enzyme, which acts as hydratase on (9Z)- and (12Z)-double bonds of C-16, C-18 non-esterified fatty acids. Products are 10-hydroxy and 10,13-dihydroxy fatty acids. Kinetic analysis suggests that FAD rather stabilizes the active conformation of the enzyme and is not directly involved in catalysis. Analysis of S. pyogenes M49 grown in the presence of either oleic or linoleic acid showed that 10-hydroxy and 10,13-dihydroxy derivatives were the only products. No further metabolism of these hydroxy fatty acids was detected. Deletion of the hydratase gene caused a 2-fold decrease in minimum inhibitory concentration against oleic acid but increased survival of the mutant strain in whole blood. Adherence and internalization properties to human keratinocytes were reduced in comparison with the wild type. Based on these results, we conclude that the previously identified MCRA protein can be classified as a FAD-containing double bond hydratase, within the carbon-oxygen lyase family, that plays a role in virulence of at least S. pyogenes M49.

    View details for DOI 10.1074/jbc.M109.081851

    View details for Web of Science ID 000276264600020

    View details for PubMedID 20145247

  • Genome-Wide Influence of Indel Substitutions on Evolution of Bacteria of the PVC Superphylum, Revealed Using a Novel Computational Method GENOME BIOLOGY AND EVOLUTION Kamneva, O. K., Liberles, D. A., Ward, N. L. 2010; 2: 870-886


    Whole-genome scans for positive Darwinian selection are widely used to detect evolution of genome novelty. Most approaches are based on evaluation of nonsynonymous to synonymous substitution rate ratio across evolutionary lineages. These methods are sensitive to saturation of synonymous sites and thus cannot be used to study evolution of distantly related organisms. In contrast, indels occur less frequently than amino acid replacements, accumulate more slowly, and can be employed to characterize evolution of diverged organisms. As indels are also subject to the forces of natural selection, they can generate functional changes through positive selection. Here, we present a new computational approach to detect selective constraints on indel substitutions at the whole-genome level for distantly related organisms. Our method is based on ancestral sequence reconstruction, takes into account the varying susceptibility of different types of secondary structure to indels, and according to simulation studies is conservative. We applied this newly developed framework to characterize the evolution of organisms of the Planctomycetes, Verrucomicrobia, Chlamydiae (PVC) bacterial superphylum. The superphylum contains organisms with unique cell biology, physiology, and diverse lifestyles. It includes bacteria with simple cell organization and more complex eukaryote-like compartmentalization. Lifestyles range from free-living organisms to obligate pathogens. In this study, we conduct a whole-genome level analysis of indel substitutions specific to evolutionary lineages of the PVC superphylum and found that indels evolved under positive selection on up to 12% of gene tree branches. We also analyzed possible functional consequences for several case studies of predicted indel events.

    View details for DOI 10.1093/gbe/evq071

    View details for Web of Science ID 000291467300028

    View details for PubMedID 21048002

  • Multidimensional analysis and functional assignment of DNA-microarray transcription profiles of genes involved in adipogenesis Biophysics Katokhin, A. V., Efimov, V. M., Badratinov, M. S., Kamneva, O. K., Mordvinov, V. A. 2006; 51 (1): 100-109