Functional Classification of cNMP-binding Proteins and Nucleotide Cyclases with Implications for Novel Regulatory Pathways in Mycobacterium tuberculosis

Abstract

We have analyzed the cyclic nucleotide (cNMP)-binding protein and nucleotide cyclase superfamilies using Bayesian computational methods of protein family identification and classification. In addition to the known cNMP-binding proteins (cNMP-dependent kinases, cNMP-gated channels, cAMP-guanine nucleotide exchange factors, and bacterial cAMP-dependent transcription factors), new functional groups of cNMP-binding proteins were identified, including putative ABC-transporter subunits, translocases, and esterases. Classification of the nucleotide cyclases revealed subtle differences in sequence conservation of the active site that distinguish the five classes of cyclases: the multicellular eukaryotic adenylyl cyclases, the eukaryotic receptor-type guanylyl cyclases, the eukaryotic soluble guanylyl cyclases, the unicellular eukaryotic and prokaryotic adenylyl cyclases, and the putative prokaryotic guanylyl cyclases. Phylogenetic distribution of the cNMP-binding proteins and cyclases was analyzed, with particular attention to the 22 complete archaeal and eubacterial genome sequences. Mycobacterium tuberculosis H37Rv and Synechocystis PCC6803 were each found to encode several more putative cNMP-binding proteins than other prokaryotes; many of these proteins are of unknown function. M. tuberculosis also encodes several more putative nucleotide cyclases than other prokaryotic species.Signal transduction pathways control many critical cellular processes, including chemotaxis, differentiation, proliferation, and apoptosis. For example, signal transduction pathways are necessary for bacterial pathogens to sense and respond to host environments, cellular differentiation during embryogenesis, conductance of nerve impulses, and cell cycle control. Disruption of these pathways can result in neoplasia, arteriosclerosis, neurological and developmental abnormalities, and cell death. The most common mechanisms of signal transduction include the phosphorylation or dephosphorylation of effector proteins by kinases and phosphatases, respectively, and the production of second messengers. Cyclic nucleotides were first recognized as second messengers 40 years ago. Such diverse molecules as (p)ppGpp, Ca 2+ , inositol triphosphate, and diacylglycerol have also been recognized as second messengers since then.The cyclic nucleotides adenosine 3Ј,5Ј-cyclic monophosphate (cAMP) and guanosine 3Ј,5Ј-cyclic monophosphate (cGMP) are key universal second messengers, mediating cellular functions in organisms as phylogenetically diverse as Escherichia coli and Homo sapiens. Intracellular concentrations of cyclic nucleotides (cNMPs) are controlled by regulation of their relative rates of synthesis, excretion, and degradation (Botsford and Harman 1992;). The nucleotide cyclases (adenylyl and guanylyl cyclase), the cNMP phosphodiesterases, and the cyclic nucleotide effector proteins (cNMP-binding proteins) have been particularly intense areas of signal transduction research, providing detailed studies of these proteins (for reviews, see Kolb et

Novel regulatory roles of cAMP receptor proteins in fast-growing environmental mycobacteria

“…For example, Mycobacterium tuberculosis harbours 16 genes encoding adenylyl cyclases (McCue et al, 2000;Shenoy et al, 2004). Consequently, intracellular cAMP concentrations in mycobacterial cells are considered to be~100-fold higher than those of other bacteria (Dass et al, 2008;Padh & Venkitasubramanian, 1976, 1980, but the significance of this is not known.…”

Mycobacterium Tuberculosis Signaling via c-AMP

“…However its signaling role in M. tuberculosis is beginning to emerge. A large number of AC genes are present in Mycobacterium tuberculosis in comparison with other microorganims (Cha et al, 2010, Klengel et al, 2005, Shenoy et al, 2004, and also that Mycobacterium just have one class III cNMP phosphodiesterase (Rv0805) that has been identified in M. tuberculosis (McCue et al, 2000, Shenoy et al, 2007 with a modest ability to efficiently hydrolyse 3′,5′-cAMP and that responds to H 2 O 2 in vitro (Bai et al, 2011, Barba et al, 2010. cAMP may serve as both an extra and intracellular signaling molecule in mycobacteria .…”

“…From these 10 cNMP binding proteins, 7 (Rv0073, Rv0104, Rv2434c, Rv2564, Rv2565, Rv3239c and Rv3728) contain an assortment of putative functional domains, including those associated with transport functions and esterase activities (McCue et al, 2000, Shenoy & Visweswariah, 2006a. Only three cNMP binding proteins have been functionally characterized to date (Bai et al, 2011).…”

“…Adelynate cyclases (ACs), which catalyze synthesis of cAMP from ATP and yield pyrophosphate as a by-product, can be classified into four different classes according to their common features: Class I cyclases, related to enterobacterial adenylate cyclases; Class II, toxic adenylate cyclases isolated from bacterial pathogens; Class III, a large and probably ancient class that comprises cyclases from both eukaryotes and prokaryotes and is strongly related to guanylate cyclases; and Class IV, with mainly one example that differs entirely from all other classes (McCue et al, 2000).…”

Decoding Human Regulatory Circuits

“…Though regulatory circuits can be defined through extensive laboratory effort, most tissues and contexts are insufficiently characterized to allow such approaches. Although pattern discovery techniques have proven effective in the identification of transcription factor binding sites (TFBSs) for several single-celled organisms (McCue et al 2000(McCue et al , 2002Rajewsky et al 2002a), successful applications in higher eukaryotes have been sparse and only partially effective (Aerts et al 2003). Transcription factors can tolerate widely varying target sequences, resulting in computational binding profiles of low specificity.…”