{"id":724,"date":"2018-04-11T18:49:33","date_gmt":"2018-04-12T01:49:33","guid":{"rendered":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/?page_id=724"},"modified":"2025-12-05T15:30:39","modified_gmt":"2025-12-05T23:30:39","slug":"research_understanding","status":"publish","type":"page","link":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/research_understanding\/","title":{"rendered":"Our Research – Main Concepts"},"content":{"rendered":"\n[et_pb_section fb_built=”1″ admin_label=”section” _builder_version=”3.0.47″][et_pb_row admin_label=”row” _builder_version=”3.0.47″ background_size=”initial” background_position=”top_left” background_repeat=”repeat”][et_pb_column type=”4_4″ _builder_version=”3.0.47″ parallax=”off” parallax_method=”on”][et_pb_text admin_label=”Text” _builder_version=”3.0.47″ background_size=”initial” background_position=”top_left” background_repeat=”repeat”]

Understanding microbial C1- metabolism<\/strong>. <\/em>Despite the great progress that has been made in our knowledge of microbial methane utilization networks, several fundamental questions remain unanswered. Based on available data, complete methane oxidation can be achieved by only three enzymes: MMO, an Xox<\/g>-type<\/g> methanol\/formaldehyde dehydrogenase, and formate dehydrogenase. However, so far all attempts to reconstruct this machinery in non-methanotrophic hosts have failed, indicating a serious gap in our knowledge of the components involved or in our understanding of how individual parts of the network are organized and cooperate. We combine systems-level approaches with classical genetics and biochemistry to establish key parts of the methanotrophic networks.<\/p>\n

 <\/p>\n

Current research projects:<\/strong><\/p>\n

EMSL (PNNL-DOE):<\/strong> Spatial organization of methane oxidation: rediscovering fundamentals<\/strong>. We rarely think about prokaryotic metabolism as a highly structured system with function-dedicated compartments. It is becoming more apparent that a bag-like representation of microbial metabolism is far from complete. A deeper understanding of a bacterial cell requires a thorough systems-level description of the subcellular network organization (enzyme complexes, compartments).\u00a0 Methane oxidation is not a simple one-enzyme process; it requires a complex network of enzymes that are dedicated to efficient energy recovery\/conservation.\u00a0 The lack of fundamental knowledge of the first steps of the methane oxidation limits our ability to model methane metabolism and interactions among microbial populations in nature, and, hence, our ability to predict factors impacting the environmental cycle of this dangerous greenhouse gas at local or global scales. It also constrains our ability to perform rational metabolic engineering of methane biocatalysis and to develop new sustainable solutions to environmental problems caused by methane emission.\u00a0 The goal of this research initiative is to gain a comprehensive knowledge of methane-oxidation machinery.\u00a0 <\/strong>Comparative, high-resolution, quantitative proteomic studies are critical for construction<\/g> of a comprehensive view of methane metabolism.<\/p>[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section]\n","protected":false},"excerpt":{"rendered":"

Understanding microbial C1- metabolism. Despite the great progress that has been made in our knowledge of microbial methane utilization networks, several fundamental questions remain unanswered. Based on available data, complete methane oxidation can be achieved by only three enzymes: MMO, an Xox-type methanol\/formaldehyde dehydrogenase, and formate dehydrogenase. However, so far all attempts to reconstruct this […]<\/p>\n","protected":false},"author":3,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"Understanding microbial C1- metabolism<\/strong>. <\/em>Despite the great progress that has been made in our knowledge of microbial methane utilization networks, several fundamental questions remain unanswered. Based on available data, complete methane oxidation can be achieved by only three enzymes: MMO, an Xox-type methanol\/formaldehyde dehydrogenase, and formate dehydrogenase. However, so far all attempts to reconstruct this machinery in non-methanotrophic hosts have failed, indicating a serious gap in our knowledge of the components involved or in our understanding of how individual parts of the network are organized and cooperate. We combine systems-level approaches with classical genetics and biochemistry to establish key parts of the methanotrophic networks.\r\n\r\n \r\n\r\nCurrent research projects:<\/strong>\r\n

ARPA-e: Process intensification of biological natural gas conversion through innovative bioreactor design.<\/strong> (in collaboration with Dr. D. Griffin, LanzaTech). The goal of this research is to establish a microbial platform for the targeted production of diesel fuel from natural gas. The research aims include (1) the metabolic engineering of a catalytic system to increase fatty acid production; and (2) the optimization of the overall fermentation process, including bioreactor design, gas-transfer, and operational parameters to obtain maximum productivity of biomass from natural gas with low input\/recycling of nutrients. Dr. Kalyuzhnaya\u2019s team contributes to the construction of novel methanotrophic traits producing long-chain alkanes and the optimization of cultivation parameters including novel sources of nitrogen (urea instead of nitrate) and sulfur (H2<\/sub>S instead of sulfate).<\/p>\r\n

DOE:<\/strong> Biogas valorization: development of a methane-to-adipic acid bioprocess.<\/strong> (in collaboration with Dr. M. Guarnieri, NREL and Dr. M. Flickinger at NCSU).\u00a0 This work is focused on the development of a methanotrophic catalyst for conversion of biogas into adipic acid, an industrially important precursor for polymer synthesis. The core of the fermentation technology is based on the metabolic alteration of carbon flux from C1<\/sub>-to-C3<\/sub> and the optimization of multiphase microchannel bioreactors, where the catalytic process happens at a phase boundary between a gas and a liquid. Dr. Kalyuzhnaya\u2019s team uses systems biology approaches to obtain a predictive understanding of flux through metabolic pathways in M. alcaliphilum <\/em>sp. 20Z involved in production and utilization of precursors to adipic acid synthesis in the context of the global metabolic network.<\/p>\r\n

NSF-CBET: Microbial conversion of greenhouse gases into fermentation-ready sugars.<\/strong> In this project we will explore a new dry fermentation process for biological methane utilization which is based on the unique ability of salt-loving, methane-consuming bacteria to not only stay active in an immobilized state without water supplementation but also to accumulate sugar (i.e., sucrose) in response to low water availability. Dry fermentation merges the full potential of biological systems with technology development to address affordable methane mitigation.\u00a0 The module is envisioned as an array of micro-fibers with active methane-consuming cells engineered to convert methane into extractable sucrose. If validated, the platform could represent a transformative solution for methane mitigation which offers the following advantages: (i) complete conversion of a significant greenhouse gas into an economically usable compound; (ii) a scalable, closed, low-complexity system; (iii) a new cost-effective approach to sustainability with the potential to convert pollution control and mitigation into an economically beneficial industry; (iv) improved life cycle parameters and the long-term sustainability of established and newly emerging bio-technologies that produce methane as a byproduct.\u00a0 The module could be developed further into air-purifying cartridges that could be implemented at any hot-spot of methane emission, as a sustainable alternative to gas flare.<\/p>\r\n

EMSL (PNNL-DOE):<\/strong> Spatial organization of methane oxidation: rediscovering fundamentals<\/strong>. We rarely think about prokaryotic metabolism as a highly structured system with function-dedicated compartments. It is becoming more apparent that a bag-like representation of microbial metabolism is far from complete. A deeper understanding of a bacterial cell requires a thorough systems-level description of the subcellular network organization (enzyme complexes, compartments).\u00a0 Methane oxidation is not a simple one-enzyme process; it requires a complex network of enzymes that are dedicated to efficient energy recovery\/conservation.\u00a0 The lack of fundamental knowledge of the first steps of the methane oxidation limits our ability to model methane metabolism and interactions among microbial populations in nature, and, hence, our ability to predict factors impacting the environmental cycle of this dangerous greenhouse gas at local or global scales. It also constrains our ability to perform rational metabolic engineering of methane biocatalysis and to develop new sustainable solutions to environmental problems caused by methane emission.\u00a0 The goal of this research initiative is to gain a comprehensive knowledge of methane-oxidation machinery.\u00a0 <\/strong>Comparative, high-resolution, quantitative proteomic studies are critical for construction of a comprehensive view of methane metabolism.<\/p>","_et_gb_content_width":"","footnotes":""},"class_list":["post-724","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-json\/wp\/v2\/pages\/724","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-json\/wp\/v2\/comments?post=724"}],"version-history":[{"count":6,"href":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-json\/wp\/v2\/pages\/724\/revisions"}],"predecessor-version":[{"id":1462,"href":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-json\/wp\/v2\/pages\/724\/revisions\/1462"}],"wp:attachment":[{"href":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-json\/wp\/v2\/media?parent=724"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}