Regulation of gene expression and metabolism in bacteria



Fernando Rojo

Group Leader



Research summary

Our aim is to characterize the global regulation networks responsible for catabolite repression, identifying their components, the signals to which they respond, and the molecular mechanisms by which they regulate gene expression. The regulatory proteins involved in these networks are different in distinct microorganisms.



Molina L, La Rosa R, Nogales J, Rojo F. Influence of the Crc global regulator on substrate uptake rates and the distribution of metabolic fluxes in Pseudomonas putida KT2440 growing in a complete medium. Environ Microbiol 2019; 21: 4446-4459.

Molina L, La Rosa R, Nogales J, Rojo F. Pseudomonas putida KT2440 metabolism undergoes sequential modifications during exponential growth in a complete medium as compounds are gradually consumed. Environ Microbiol 2019; 21: 2375-2390.

Val-Calvo J, Luque-Ortega JR, Crespo I, Miguel-Arribas A, Abia D, Sánchez-Hevia D, Serrano E, Gago-Córdoba C, Ares S, Alfonso C, Rojo F, Wu LJ, Boer R, Meijer WJJ. Novel regulatory mechanism of establishment genes of conjugative plasmids. Nucleic Acids Res 2018; 46: 11910-11926.

Sánchez-Hevia D, Yuste L, Moreno R, Rojo F. Influence of the Hfq and Crc global regulators on the control of iron homeostasis in Pseudomonas putida. Environ Microbiol 2018; 20: 3484-3503.

Sevilla E, Yuste L, Moreno R, Rojo F. Differential expression of the three Alcanivorax borkumensis SK2 genes coding for the three P450 cytochromes involved in the assimilation of hydrocarbons. Environ Microbiol Rep 2017; 9: 797-808.

More Publications


To be competitive in the environments they colonize, bacteria must optimize metabolism to attain maximum gain from available nutrients at minimum energetic cost. Not all potential carbon sources are equally effective in this respect. Probably for this reason, when confronted with a mixture of potentially assimilable compounds at sufficient concentrations, many bacteria preferentially use one of them, leaving others aside until the preferred compound is consumed. This selection implies a complex regulatory process termed catabolite repression. Unravelling the molecular mechanisms that underlie these regulatory events helps us comprehend how bacteria coordinate their metabolism and gene expression programmes and optimize growth. It also aids in the design and optimization of biotechnological processes, and to understand how bacteria degrade compounds in nature.

This is particularly true for compounds that are difficult to degrade and thus accumulate in the environment, posing pollution problems. Hydrocarbons are a clear example of this kind of non-preferred compounds. The regulatory proteins and molecular mechanisms responsible for catabolite repression differ among microorganisms. Our work focuses on Pseudomonas putida, a bacterium that has a very versatile metabolism, colonizes very diverse habitats, and is widely used in biotechnology. In the last few years, we have been analysing a regulatory network that relies on the Crc and Hfq proteins, which ultimately inhibit translation of mRNAs containing a specific A-rich sequence motif within their translation initiation region. Two small RNAs termed CrcZ and CrcY, the levels of which vary greatly depending on growth conditions, antagonize the inhibitory effect of Hfq and Crc. We aim to characterize the influence of Crc, Hfq, CrcZ and CrcY on P. putida physiology, the signals to which they respond, and the molecular mechanisms by which they regulate gene expression. We intend to determine how they modulate metabolism in response to fluctuating environmental conditions.






Fernando Rojo Principal investigator
Renata Moreno Senior scientist
Sofía Hernández Postdoctoral scientist
Ruggero La Rosa Predoctoral scientist
Dione Sánchez Predoctoral scientist
Luis Yuste Technicians

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