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Possible chemotaxis in comparative genomics a b

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Mónica Marcela Galicia-Jiménez , Rafael Rojas-Herrera , Carlos Sandoval-Castro & Héctor Magaña-Sevilla a Instituto de Genética, Universidad del Mar. Campus Puerto Escondido. Ciudad Universitaria, Carretera Vía Sola de Vega, Puerto Escondido, San Pedro Mixtepec, Juquila, Oax, C.P, 71980, México b Facultad de Ingeniería Química, Universidad Autónoma de Yucatán Periférico, Mérida, México c Facultad de Medicina Veterinaria y Zootecnìa, Universidad Autónoma de Yucatán, Mérida, México d Instituto Tecnológico de Conkal, Centro de Cómputo, Conkal, México Available online: 08 Aug 2011

To cite this article: Mónica Marcela Galicia-Jiménez, Rafael Rojas-Herrera, Carlos Sandoval-Castro & Héctor MagañaSevilla (2011): Possible chemotaxis in Ruminococcus albus: comparative genomics, Journal of Applied Animal Research, 39:3, 189-191 To link to this article: http://dx.doi.org/10.1080/09712119.2011.607705

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Journal of Applied Animal Research, Vol. 39, No. 3, September 2011, 189 191

Possible chemotaxis in Ruminococcus albus: comparative genomics Monica Marcela Galicia-Jimenez a,b, Rafael Rojas-Herrerac, Carlos Sandoval-Castrod and Hector Magana-Sevilla* a

Instituto de Gene´tica. Universidad del Mar. Campus Puerto Escondido. Ciudad Universitaria, Carretera Vi´a Sola de Vega, Puerto Escondido, San Pedro Mixtepec, Juquila, Oax., Me´xico C.P. 71980; bFacultad de Ingenier ´a Qu ´mica, Universidad Auto´noma de Yucata´n Perife´rico, Me´rida, Me´xico; cFacultad de Medicina Veterinaria y Zootecn `a, Universidad Auto´noma de Yucata´n, Me´rida, Me´xico dInstituto Tecnolo´gico de Conkal, Centro de Co´mputo, Conkal, Me´xico (Received 9 October 2010; final version received 31 January 2011) Several comparative genomic tools were used to determine the existence of chemiotaxis in ruminal bacteria. Comparative analysis of microbial genomes (database comprehensive microbial resource (CMR)) was used to search for a specific chemiotaxis gene. Then, short sequences of Ruminococcus albus were searched in the database of the National Center for Biotechnology Information, and compared them in the and Concise Microbial Protein. To predict the number of trans-membrane helices of the putative protein, the methyl-accepting chemotaxis proteins (MCP)program was used (TMpred and TopPred). For comparisons of putative protein structures in the MCP and chemotaxis protein, Simple Modular Architecture Research Tool and protein families database were used. Short sequences of the genome of R. albus revealed the presence of chemotaxis genes that could encode a chemoreceptor (MCP)and chemotaxis proteins. Groups of R. albus chemotaxis genes may be responsible for a diverse set of signalling functions, such as the formation of biofilm, adhesion and gene regulation. Keywords: Chemotaxis; Ruminococcus albus; MCPs

Introduction Chemotaxis is a process mediated by a set of chemoreceptors that transmit chemical stimuli through a signal-transduction system transforming bacterial behaviour in response. Proteins related to this system are arranged in four groups (1)recognition and signal transduction, (2)excitation, (3) adaptation and (4)removal signal. Escherichia coli is the principal model for understanding this system, which is made up of two components comprising a receptor protein (methyl-accepting chemotaxis proteins, (MCPs), when the stimulus (ligand) binds to a conformational change in place. MCP protein in turn translates the information into the intracellular signalling domain histidine kinase autophosphorylated protein (CheA), once CheA-P is a substrate of cytoplasmic response regulator Che Y. The resulting CheY-P interacts with the flagellar motor mechanism (FliM), which induces a change in the direction of rotation of the flagellum (counter clockwise)as the increase in the concentration of attractant lowers the levels of CheY-P. This is reflected in the swimming of the bacteria towards favourable (Stock and Levit 2000; Wolanin et al. 2002; Szurmant and Ordal 2004). Ruminococcus albus is a Gram-positive, strictly anaerobic, motile, cellulolytic and isolated from the rumen. This bacterium requires fenilpropionicos and *Corresponding author. Email: [email protected] ISSN 0971-2119 print/ISSN 0974-1844 online # 2011 Taylor & Francis http://dx.doi.org/10.1080/09712119.2011.607705 http://www.tandfonline.com

phenylacetic acid for maximum growth. No doubt that the complete sequencing of several microbial genomes has deepened the understanding of bacterial physiology. However, knowledge of the molecular mechanisms that control chemotaxis is limited. Nevertheless, genomic studies have enabled the identification and comparison between different proteins sequences possibly involved in this type of behaviour. We predict by comparison of homologous genes of known function from other species, genes that could encode putative chemotactic proteins, fragments of the genome sequences of R. albus 8, which may confer a R. albus potential benefits among which are a greater efficiency in the colonisation and degradation of food particles of ruminants.

Materials and methods To search for chemotaxis gene sequences used in R. albus database comparative analysis of microbial genomes (CMR) (http://cmr.jcvi.org/cgi-bin/CMR/ CmrHomePage.cgi)(Uchiyama 2003)was used. Short sequences of R. albus 8 in the database National Center for Biotechnology Information http:// www.ncbi.nlm.nih.gov/genomes/lproks.cgi were also searched (Wheeler et al. 2006)and compared them in the database comprehensive microbial resource