Education

• B.Sc. 2004, Beijing Normal University, Beijing, China
• Ph.D. 2011, Sanford-Burnham Medical Research Institute, La Jolla, CA

Overview

Bacteria are among the most abundant organisms on Earth. In the ocean, bacteria play important roles in primary production, respiration, as well as the cycling of various phosphorus, nitrogen, and sulfur-containing nutrients. Besides their contributions to global nutrient cycles, bacteria respond very quickly to environmental changes. Therefore, our understanding on the function and adaptation of marine bacteria can provide significant insights into how the marine environment is changing and how these changes will affect nutrient distribution and hence stability and survival of marine lives.

Our laboratory aims at constructing computational models to understand the formation, settlement, and evolution of bacterial communities in various marine environments and to predict their responses to environmental stresses. Specifically, we have three main objectives: (1) Genomic comparison of marine bacteria to search for environmental-specific adaptations; (2) Metabolic network modeling that permits the simulation of biomass production and nutrient turnover at various environmental conditions; (3) Development of computational tools that can be widely used for the processing of “Omics” data and the simulation of biological networks.

Research Areas

Genomic and Functional Diversity of Epsilonproteobacteria

Epsilonproteobacteria are a metabolically versatile class that maintain different life styles including free-living as well as forming mutualistic or parasitic associations with other organisms. At deep-sea hydrothermal vents, species of this class fix inorganic carbon into organic compounds using geochemical energy sources, serving as dominant primary producers in such dark marine environments. At coastal and open ocean environments, they play important roles in the cycling of various carbon, sulfur and nitrogen containing nutrients. At human digestive systems, they can exist asymptomatically or cause diseases like peptic ulcers or gastric cancer. The global relevance of Epsilonproteobacteria has not been recognized until the past decade. For a long time, studies have been focused on the pathogenic species, such as those of the genera Helicobacter and Campylobacter. As more and more species were identified and isolated in the natural environment, today Epsilonproteobacteria is known to play important roles in the cycling of sulphidic compounds at various marine and terrestrial aquatic environments. We ask two questions in the analyses of Epsilonproteobacteria. First, what dominates the genomic evolution of this class, the preservation of genes from common ancestry or the acquisition of genes from the environment? Second, how can the presence and absence of genes tell us about the metabolic needs of organisms in the natural environment? We performed a large-scale comparison of 39 fully sequenced genomes to examine these two questions.

Selected Publications

• Kazanov MD, Igarashi Y, Eroshkin AM, Cieplak P, Ratnikov B, Zhang Y, Li Z, Godzik A, Osterman AL, Smith JW. (2011) Structural determinants of limited proteolysis.Journal of Proteome Research 10(8): 3642-51.
• Zhang Y, Zagnitko O, Rodionova I, Osterman A, Godzik A. (2011) The FGGY carbohydrate kinase family: insights into the evolution of functional specificities. PLoS Computational Biology 7(12): e1002318.
• Igarashi Y, Heureux E, Doctor KS, Talwar P, Gramatikova S, Gramatikoff K, Zhang Y, Blinov M, Ibragimova SS, Boyd S, Ratnikov B, Cieplak P, Godzik A, Smith JW, Osterman AL, Eroshkin AM. (2009). PMAP: databases for analyzing proteolytic events and pathways. Nucleic Acids Research 37, D611-8. Blinov M, Ibragimova SS, Boyd S, Ratnikov B, Cieplak P, Godzik A, Smith JW, Osterman AL, Eroshkin AM. (2009). PMAP: databases for analyzing proteolytic events and pathways. Nucleic Acids Research 37, D611-8.
• Burra PV, Zhang Y, Godzik A, Stec B. (2009) Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure. Proc. Natl. Acad. Sci. U. S. A. 106, 10505-10.
• Zhang Y, Thiele I, Weekes D, Li Z, Jaroszewski L, Ginalski K, Deacon AM, Wooley J, Lesley SA, Wilson IA, Palsson B, Osterman A, Godzik A. (2009) Three-dimensional structural view of the central metabolic network of Thermotoga maritima. Science 325, 1544-1549.
• Igarashi Y, Eroshkin A, Gramatikova S, Gramatikoff K, Zhang Y, Smith JW, Osterman AL, and Godzik A. (2007). CutDB: a proteolytic event database. Nucleic Acids Research 35, D546-549.
• Zhang Y, Stec B, and Godzik A. (2007). Between order and disorder in protein structures: analysis of “dual personality” fragments in proteins. Structure 15, 1141- 1147.