Hypothetical pictorial representation of horizontal gene transfer of NACHT NTPase genes in early green plants.

<p>Probabe horizontal gene transfer (HGT) of NACHT NTPase from cyanobacterial ancestor to early green plant lineages. The NACHT NTPase occurs in all three major kingdoms of life that arose from single progenote and may have acquired in single-celled green alage (chlorophytes) through HGT from an ancestor of cyanobacteria (<i>Nostoc</i> sp.).</p

Genome-wide survey of 67 organisms for NB-ARC and NACHT NTPases.

<p>The genome-wide survey of 67 diverse organisms shows the presence (+) or absence (-) of NB-ARC and NACHT NTPases in respective organism.</p

Structural comparison of NACHT of <i>Selaginella moellendorffii</i> with NLRC4 NACHT.

<p>The superposition of NACHT of <i>S</i>. <i>moellendorffii</i> with NLRC4 NACHT using TM-align. (a) NLRC4 NACHT and 407161|PACid:15416689 (b) NLRC4 NACHT and 425148|PACid:15402815. Red colour cartoon shows NLRC4 NACHT and green colour cartoons show <i>S</i>. <i>moellendorffii</i> NACHT domains. The residue range for Walker-A and Walker-B are 169–176 and 244–252 (NLRC4 NACHT); 82–89 and 169–177 (407161|PACid:15416689); 161–168 and 238–245 (425148|PACid:15402815) respectively. The quality of model was assessed on basis of c-score and TM-score. The predicted value of c-score and TM-score by I-TASSER are -1.36 and 0.55+-0.15 for 407161|PACid:15416689 and are -2.74 and 0.40+-0.13 for 425148|PACid:15402815. The root mean square deviation (RMSD) calculated by TM-align are 0.79 and 0.74 for 407161|PACid:15416689 and 425148|PACid:15402815 respectively.</p

List of NACHT domain containing protein sequences in early green plants.

<p>List of NACHT domain containing protein sequences in early green plants.</p

Multiple Sequence Alignment of NACHT NTPases.

<p>Multiple sequence alignment (MSA) for NACHT of <i>Selaginella moellendorffii</i>, <i>Physcomitrella patens</i>, green algae, cyanobacteria and NLRC4 showing the conserved region at the site of Walker-A and Walker-B and other motifs [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0150634#pone.0150634.ref010" target="_blank">10</a>]. (The S_moe_* denotes NACHT NTPases in <i>S</i>. <i>moellendorffii</i>, C_re_* for <i>C</i>. <i>reinhairdtii</i> and C_sub_* for <i>C</i>. s<i>ubellipsoidea</i> where * represents any integer number). More than 80% consensus background coloring of amino acid residues reflects as follows: hydrophobic residues (ACFILMVWY), aromatic residues (FHWY), and aliphatic residues (VIL) are shaded cyan/blue; polar residues (STQN) are colored green; acidic residues (DE) are colored magenta; basic residues (KR) are colored red; Glycine (G) is shaded with mustard color; and Proline (P) is colored yellow.</p

Phylogenetic tree of NB-ARC and NACHT NTPases in <i>Selaginella moellendorffii</i>.

<p>The NACHT and NB-ARC of <i>S</i>. <i>moellendorffii</i> were aligned using ClustalW and phylogenetic tree was constructed using MEGA v5.2.2. The green lines represents the NB-ARC AP-ATPases and blue lines denotes NACHT NTPases proteins forming two separate clades. The members of both NACHT and NB-ARC NTPase grouped discretely supporting the independent evolution of these STAND P-loop NTPases.</p

Unrooted phylogenetic tree of NB-ARC and NACHT NTPases.

<p>The members of NACHT and NB-ARC NTPases of <i>S</i>. <i>moellendorffii</i> were aligned with NACHT NTPases of green algae, cyanobacteria and <i>Physcomitrella patens</i> using ClustalW v2.1 and a phylogenetic tree was constructed by employing MEGA v5.2.2. The NLRC4 NACHT was taken as representative of NACHT and APAF1 NB-ARC as NB-ARC representative. (The S_moe_* denotes NACHT NTPases and NB-ARC AP-ATPases in <i>S</i>. <i>moellendorffii</i>, C_re_* for <i>C</i>. <i>reinhairdtii</i> and C_sub_* for <i>C</i>. s<i>ubellipsoidea</i> where * represents any integer number.)</p

Unrooted phylogenetic tree of NACHT NTPases from diverse organisms of three major kingdoms of life.

<p>The multiple sequence alignment was performed for putative NACHT NTPases in early green plants (green algae, bryophyte, and lycophyte) and well-known NACHT NTPases in other organisms including bacteria, archaebacteria, cyanobacteria, protozoa, fungi, and chordates and phylogenetic tree was constructed using MEGA v5.2.2. The phylogenetic analysis shows that NACHT NTPases of early green plant were grouped in a clan of NACHT NTPases of cyanobacteria or fungi (in clades III, IV, V, VI, and III). Moreover, results of delta-blast search of NACHT NTPase in <i>C</i>. <i>reinhardtii</i> revealed the the top hits with <i>Nostoc</i> sp PCC 7120. From phyletic patterns and delta-blast search results from the present study, we infers that the DNA for NACHT in green algae may have been transferred from the ancestors of extant cyanobacteria.</p

Phylogenetic tree of NB-ARC and NACHT NTPases of three major kingdoms of life.

<p>The NB-ARC and NACHT NTPases present in the diverse organisms were aligned by ClustalW v2.1 and phylogenetic tree was constructed by employing RAxML version 7.2.8-ALPHA. The phylogenetic tree was visualized using MEGA v5.2.2. Green and red branches denote the NB-ARC AP-ATPase and NACHT NTPase group respectively. The phylogenetic analysis inferred that few members of STAND P-loop NTPase of plants were making a clan in NACHT NTPase group, are putative NACHT NTPase of plants.</p

Physical Modelling of Flow and Dispersion in Urban Canopy

Katedra fyziky atmosféryDepartment of Atmospheric PhysicsFaculty of Mathematics and PhysicsMatematicko-fyzikální fakult