Cyanobacterial response regulator PatA contains a conserved N-terminal domain (PATAN) with an alpha-helical insertion

The cyanobacterium Anabaena (Nostoc) PCC 7120 responds to starvation for nitrogen compounds by differentiating approximately every 10th cell in the filament into nitrogen-fixing cells called heterocysts. Heterocyst formation is subject to complex regulation, which involves an unusual response regulator PatA that contains a CheY-like phosphoacceptor (receiver, REC) domain at its C-terminus. PatA-like response regulators are widespread in cyanobacteria; one of them regulates phototaxis in Synechocystis PCC 6803. Sequence analysis of PatA revealed, in addition to the REC domain, a previously undetected, conserved domain, which we named PATAN (after PatA N-terminus), and a potential helix-turn-helix (HTH) domain. PATAN domains are encoded in a variety of environmental bacteria and archaea, often in several copies per genome, and are typically associated with REC, Roadblock and other signal transduction domains, or with DNA-binding HTH domains. Many PATAN domains contain insertions of a small additional domain, termed alpha-clip, which is predicted to form a four-helix bundle. PATAN domains appear to participate in protein-protein interactions that regulate gliding motility and processes of cell development and differentiation in cyanobacteria and some proteobacteria, such as Myxococcus xanthus and Geobacter sulfurreducens.

[1]  Jason M. Link,et al.  MglA, a small GTPase, interacts with a tyrosine kinase to control type IV pili‐mediated motility and development of Myxococcus xanthus , 2002, Molecular microbiology.

[2]  M. Ohmori,et al.  Identification of Low-temperature-regulated ORFs in the cyanobacterium Anabaena sp. strain PCC 7120: distinguishing the effects of low temperature from the effects of photosystem II excitation pressure. , 2005, Plant & cell physiology.

[3]  Michael Y. Galperin,et al.  A census of membrane-bound and intracellular signal transduction proteins in bacteria: Bacterial IQ, extroverts and introverts , 2005, BMC Microbiology.

[4]  Michael Y. Galperin,et al.  The COG database: a tool for genome-scale analysis of protein functions and evolution , 2000, Nucleic Acids Res..

[5]  Michael Y. Galperin.  Structural Classification of Bacterial Response Regulators: Diversity of Output Domains and Domain Combinations , 2006, Journal of bacteriology.

[6]  Yeh Chen,et al.  Structure and Function of the XpsE N-Terminal Domain, an Essential Component of the Xanthomonas campestris Type II Secretion System* , 2005, Journal of Biological Chemistry.

[7]  Michael Y. Galperin,et al.  Bacterial signal transduction network in a genomic perspective. , 2004, Environmental microbiology.

[8]  D. Barford,et al.  Topological characteristics of helical repeat proteins. , 1999, Current opinion in structural biology.

[9]  M. Ikeuchi,et al.  Novel putative photoreceptor and regulatory genes Required for the positive phototactic movement of the unicellular motile cyanobacterium Synechocystis sp. PCC 6803. , 2000, Plant & cell physiology.

[10]  H. Kaplan.  Multicellular development and gliding motility in Myxococcus xanthus. , 2003, Current opinion in microbiology.

[11]  P. Youderian,et al.  Identification of genes required for adventurous gliding motility in Myxococcus xanthus with the transposable element mariner , 2003, Molecular microbiology.

[12]  M. Cygler,et al.  The Structure of the MAPK Scaffold, MP1, Bound to Its Partner, p14 , 2004, Journal of Biological Chemistry.

[13]  S. Laurent,et al.  Heterocyst differentiation and pattern formation in cyanobacteria: a chorus of signals , 2006, Molecular microbiology.

[14]  R. Haselkorn,et al.  The patA gene product, which contains a region similar to CheY of Escherichia coli, controls heterocyst pattern formation in the cyanobacterium Anabaena 7120. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[15]  Igor B. Zhulin,et al.  Four-helix bundle: a ubiquitous sensory module in prokaryotic signal transduction , 2005, Bioinform..

[16]  J. Meeks,et al.  Regulation of Cellular Differentiation in Filamentous Cyanobacteria in Free-Living and Plant-Associated Symbiotic Growth States , 2002, Microbiology and Molecular Biology Reviews.

[17]  L. Søgaard‐Andersen.  Cell polarity, intercellular signalling and morphogenetic cell movements in Myxococcus xanthus. , 2004, Current opinion in microbiology.

[18]  Developmental Aggregation of Myxococcus xanthus Requires frgA, anfrz-Related Gene , 2000, Journal of bacteriology.

[19]  Y. Nakamura,et al.  Complete genomic sequence of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120. , 2001, DNA research : an international journal for rapid publication of reports on genes and genomes.

[20]  Y. Kanesaki,et al.  The pathway for perception and transduction of low‐temperature signals in Synechocystis , 2000, The EMBO journal.

[21]  R. Haselkorn.  How Cyanobacteria Count to 10 , 1998, Science.

[22]  M. Ohmori,et al.  Genome-wide expression analysis of the responses to nitrogen deprivation in the heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120. , 2003, DNA research : an international journal for rapid publication of reports on genes and genomes.

[23]  D. Kehoe,et al.  Genomic DNA Microarray Analysis: Identification of New Genes Regulated by Light Color in the Cyanobacterium Fremyella diplosiphon , 2004, Journal of bacteriology.

[24]  Geoffrey J. Barton,et al.  JPred : a consensus secondary structure prediction server , 1999 .

[25]  D. G. Adams,et al.  Heterocyst formation in cyanobacteria. , 2000, Current opinion in microbiology.

[26]  Robert D. Finn,et al.  The Pfam protein families database , 2004, Nucleic Acids Res..

[27]  L. Goldstein,et al.  Drosophila roadblock and Chlamydomonas Lc7 , 1999, The Journal of cell biology.

[28]  C. Wolk,et al.  Heterocyst formation. , 1996, Annual review of genetics.

[29]  C. Ponting,et al.  The GAF domain: an evolutionary link between diverse phototransducing proteins. , 1997, Trends in biochemical sciences.

[30]  E. Koonin,et al.  Dynein light chains of the Roadblock/LC7 group belong to an ancient protein superfamily implicated in NTPase regulation , 2000, Current Biology.

[31]  I. Zhulin,et al.  PAS Domains: Internal Sensors of Oxygen, Redox Potential, and Light , 1999, Microbiology and Molecular Biology Reviews.

[32]  Sébastien Carrère,et al.  The ProDom database of protein domain families: more emphasis on 3D , 2004, Nucleic Acids Res..

[33]  A. Pugsley,et al.  Multiple Interactions between Pullulanase Secreton Components Involved in Stabilization and Cytoplasmic Membrane Association of PulE , 2000, Journal of bacteriology.

[34]  M. Sternberg,et al.  Enhanced genome annotation using structural profiles in the program 3D-PSSM. , 2000, Journal of molecular biology.

[35]  Structure of the GAF domain, a ubiquitous signaling motif and a new class of cyclic GMP receptor , 2000, The EMBO journal.

[36]  D. Bhaya,et al.  Light regulation of type IV pilus-dependent motility by chemosensor-like elements in Synechocystis PCC6803 , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[37]  Ho-Sung Yoon,et al.  Heterocyst development in Anabaena. , 2003, Current opinion in microbiology.

[38]  D T Jones,et al.  Protein secondary structure prediction based on position-specific scoring matrices. , 1999, Journal of molecular biology.