Regulation of gene expression and metabolism in bacteria

FRojo

 

Fernando Rojo

Group Leader

Contact

 

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.

 

Publications

Gómez-García G, Ruiz-Enamorado A, Yuste L, Rojo F*, Moreno R*. Expression of the ISPpu9 transposase from Pseudomonas putida KT2440 is regulated by two small RNAs and a long and structured 5´-untranslated regionNucleic Acids Research 2021; 49: 9211-9228

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.

More Publications

 

To be competitive in the environments they colonise, bacteria must optimise metabolism to attain maximum gain from available nutrients. Not all potential carbon sources are equally effective in this respect. 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 one is consumed. This implies a complex regulatory process termed catabolite repression. Unravelling the molecular mechanisms involved helps understanding how bacteria coordinate their metabolism and gene expression programs and optimise growth. It also aids in the design and optimisation of biotechnological processes and to understand how bacteria degrade compounds in Nature.

The regulators and molecular mechanisms responsible for catabolite repression differ among microorganisms. Our work is focused on Pseudomonas putida, a bacterium with a versatile and robust metabolism much used in biotechnology. Catabolite repression relies on a complex regulatory network that includes the Crc and Hfq proteins, which inhibit translation of mRNAs containing a specific A-rich sequence motif within their translation initiation region. Two small RNAs, CrcZ and CrcY, the levels of which vary greatly depending on growth conditions, antagonise the inhibitory effect of Hfq and Crc. Our aim is to characterise the influence of Crc, Hfq, CrcZ and CrcY in the physiology of P. putida, the signals to which they respond, and the molecular mechanisms by which they regulate gene expression.

In addition, we have analysed the role of Hfq in other processes such as iron homeostasis and the regulation of ISPpu9, an insertion sequence of P. putida KT2440 in which we have observed that translation of the transposase gene mRNA is inhibited by a highly structured 5’ untranslated region, effect that is counteracted by an antisense small RNA and further modulated by a second small RNAs.

 

Rojo F fig1

Figure legend. Effect of inactivating the crc gene on the configuration of the metabolite fluxes related to central carbon metabolism during early, mid and late exponential growth. The fluxes that increased (in red), decreased (in green), or remained unchanged (in black) in the Crc-null strain as compared to the wild type, are highlighted. Compounds that were released to the medium and later recycled are indicated in blue. 

 

grupoRojoRed2 

Name
Position
Contact
Fernando Rojo Principal investigator
Renata Moreno Senior scientist
Elva Quiroz Postdoctoral scientist
Guillermo Gómez Predoctoral scientist
Elena Pares Predoctoral scientist
Luis Yuste Technician

NOTE! This site uses cookies and similar technologies.

If you continue browsing or do not change browser settings, we consider your acepptance for using. Learn more

I understand

COOKIES POLICY

A cookie is a text file that is stored on your computer or mobile device via a web server and only that server will be able to retrieve or read the contents of the cookie and allow the Web site remember browser preferences and navigate efficiently. Cookies make the interaction between the user and the website faster and easier.

General information

This Website uses cookies. Cookies are small text files generated by the web pages you visit, which contain the session data that can be useful later in the website. In this way this Web remembers information about your visit, which can facilitate your next visit and make the website more useful.

How do cookies?

Cookies can only store text, usually always anonymous and encrypted. No personal information is ever stored in a cookie, or can be associated with identified or identifiable person.

The data allow this website to keep your information between the pages, and also to discuss how to interact with the website. Cookies are safe because they can only store information that is put there by the browser, which is information the user entered in the browser or included in the page request. You can not run the code and can not be used to access your computer. If a website encrypts cookie data, only the website can read the information.

What types of cookies used?

The cookies used by this website can be distinguished by the following criteria:

1. Types of cookies as the entity that manages:

Depending on who the entity operating the computer or domain where cookies are sent and treat the data obtained, we can distinguish:

- Own cookies: are those that are sent to the user's terminal equipment from a computer or domain managed by the editor itself and from which provides the service requested by the user.

- Third party cookies: these are those that are sent to the user's terminal equipment from a machine or domain that is not managed by the publisher, but by another entity data is obtained through cookies.

In the event that the cookies are installed from a computer or domain managed by the editor itself but the information collected by these is managed by a third party can not be considered as party cookies.

2. Types of cookies as the length of time that remain active:

Depending on the length of time that remain active in the terminal equipment can be distinguished:

- Session cookies: cookies are a type designed to collect and store data while the user accesses a web page. Are usually used to store information that only worth preserving for the service requested by the user at any one time (eg a list of products purchased).

- Persistent cookies: cookies are a type of data which are stored in the terminal and can be accessed and treated for a period defined by the head of the cookie, and can range from a few minutes to several years.

3. Cookies types according to their purpose:

Depending on the purpose for which the data are processed through cookies, we can distinguish between:

- Technical cookies: these are those that allow the user to navigate through a web page or application platform and the use of different options or services it exist as, for example, control traffic and data communication, identify the session, access to restricted access parts, remember the elements of an order, make the buying process an order, make an application for registration or participation in an event, use security features while browsing store content for dissemination videos or sound or share content via social networks.

- Customization cookies: these are those that allow the user to access the service with some general characteristics based on a predefined set of criteria in the user terminal would eg language, the type of browser through which you access the service, the locale from which you access the service, etc.

- Analysis cookies: they are those that allow the responsible for them, monitoring and analyzing the behavior of users of the web sites that are linked. The information gathered through such cookies are used in measuring the activity of web sites, application or platform and for the profiling of user navigation of such sites, applications and platforms, in order to make improvements function data analysis how users use the service.

Management tool cookies

This Website uses Google Analytics.

Google Analytics is a free tool from Google that primarily allows website owners know how users interact with your website. Also, enable cookies in the domain of the site in which you are and uses a set of cookies called "__utma" and "__utmz" to collect information anonymously and reporting of website trends without identifying individual users..

For statistics of use of this website use cookies in order to know the level of recurrence of our visitors and more interesting content. This way we can concentrate our efforts on improving the most visited areas and make the user more easily find what they are looking for. On this site you can use the information from your visit for statistical evaluations and calculations anonymous data and to ensure the continuity of service or to make improvements to their websites. For more details, see the link below privacy policy [http://www.google.com/intl/en/policies/privacy/]

How to manage cookies on your computer: disabling and deleting cookies

All Internet browsers allow you to limit the behavior of a cookie or disable cookies within settings or browser settings. The steps for doing so are different for each browser, you can find instructions in the help menu of your browser.

If you decline the use of cookies, since it is possible thanks to the preferences menu of your browser or settings, reject, this website will continue to function properly without the use of the same.

Can you allow, block or delete cookies installed on your computer by setting your browser options installed on your computer:

- For more information about Internet Explorer click here.
- For more information on Chrome click here.
- For more information about Safari click here.
- For more information about Firefox click here.

Through your browser, you can also view the cookies that are on your computer, and delete them as you see fit. Cookies are text files, you can open and read the contents. The data within them is almost always encrypted with a numeric key corresponding to an Internet session so often has no meaning beyond the website who wrote it.

Informed consent

The use of this website on the other hand, implies that you paid your specific consent to the use of cookies, on the terms and conditions provided in this Cookies Policy, without prejudice to the measures of deactivation and removal of cookies that you can take, and mentioned in the previous section.