title: Systems biology of bacterial nitrogen fixation: high-throughput technology and its integrative description with constraint-based modeling.
abstract: BACKGROUND
  Bacterial nitrogen fixation is the biological process by which atmospheric nitrogen is uptaken by bacteroids located in plant root nodules and converted into ammonium through the enzymatic activity of nitrogenase. In practice, this biological process serves as a natural form of fertilization and its optimization has significant implications in sustainable agricultural programs. Currently, the advent of high-throughput technology supplies with valuable data that contribute to understanding the metabolic activity during bacterial nitrogen fixation. This undertaking is not trivial, and the development of computational methods useful in accomplishing an integrative, descriptive and predictive framework is a crucial issue to decoding the principles that regulated the metabolic activity of this biological process.
  
  
  RESULTS
  In this work we present a systems biology description of the metabolic activity in bacterial nitrogen fixation. This was accomplished by an integrative analysis involving high-throughput data and constraint-based modeling to characterize the metabolic activity in Rhizobium etli bacteroids located at the root nodules of Phaseolus vulgaris (bean plant). Proteome and transcriptome technologies led us to identify 415 proteins and 689 up-regulated genes that orchestrate this biological process. Taking into account these data, we: 1) extended the metabolic reconstruction reported for R. etli; 2) simulated the metabolic activity during symbiotic nitrogen fixation; and 3) evaluated the in silico results in terms of bacteria phenotype. Notably, constraint-based modeling simulated nitrogen fixation activity in such a way that 76.83% of the enzymes and 69.48% of the genes were experimentally justified. Finally, to further assess the predictive scope of the computational model, gene deletion analysis was carried out on nine metabolic enzymes. Our model concluded that an altered metabolic activity on these enzymes induced different effects in nitrogen fixation, all of these in qualitative agreement with observations made in R. etli and other Rhizobiaceas.
  
  
  CONCLUSIONS
  In this work we present a genome scale study of the metabolic activity in bacterial nitrogen fixation. This approach leads us to construct a computational model that serves as a guide for 1) integrating high-throughput data, 2) describing and predicting metabolic activity, and 3) designing experiments to explore the genotype-phenotype relationship in bacterial nitrogen fixation.
authors.affiliation: Programa de Genomica Funcional de Procariotes, Centro de Ciencias Genómicas-UNAM, Av, Universidad s/n, Col, Chamilpa, Cuernavaca Morelos, C,P, 62210, Mexico. resendis@ccg.unam.mx
authors.forename: Osbaldo
authors.initials: O
authors.lastname: Resendis-Antonio
authors.forename: Magdalena
authors.initials: M
authors.lastname: Hernández
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Salazar
authors.forename: Sandra
authors.initials: S
authors.lastname: Contreras
authors.forename: Gabriel Martínez
authors.initials: GM
authors.lastname: Batallar
authors.forename: Yolanda
authors.initials: Y
authors.lastname: Mora
authors.forename: Sergio
authors.initials: S
authors.lastname: Encarnación
mesh_terms: D015964:Gene Expression Regulation, Bacterial / Q000235:genetics / Q000502:physiology; D013058:Mass Spectrometry; D053858:Metabolic Networks and Pathways / Q000235:genetics / Q000502:physiology*; D046228:Microarray Analysis; D008954:Models, Biological; D009586:Nitrogen Fixation / Q000235:genetics / Q000502:physiology*; D027805:Phaseolus / Q000382:microbiology*; D040901:Proteomics / Q000379:methods; D042163:Rhizobium etli / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D053204:Root Nodules, Plant / Q000382:microbiology*; D049490:Systems Biology / Q000379:methods*