Comparative Genomics of Myxobacterial Chemosensory Systems

Abstract

Chemosensory systems (CSS) are among the most complex organizations of proteins functioning cooperatively to regulate bacterial motility and other cellular activities. These systems have been studied extensively in bacteria, and usually, they are present as a single system. Eight CSS, the highest number in bacteria, have been reported in DK1622 and are involved in coordinating diverse functions. Here, we have explored and compared the CSS in all available genomes of order members contain 97 to 476 two-component system (TCS) proteins, which assist the bacteria in surviving and adapting to varying environmental conditions. The number of myxobacterial CSS ranges between 1 and 12, with the largest number in family and the smallest in CheA protein was used as a phylogenetic marker to infer evolutionary relatedness between different CSS, and six novel CSS ("extra CSS" [ECSS]) were thus identified in the myxobacteria besides the previously reported Che1 to Che8 systems from Che1 to Che8 systems are monophyletic to deltaproteobacteria, whereas the newly identified ECSS form separate clades with different bacterial classes. The comparative modular organization was concordant with the phylogeny. Four clusters lacking CheA proteins were also identified via CheB-based phylogenetic analysis and were categorized as accessory CSS (ACSS). In, an orphan CSS was identified, in which both CheA and CheB were absent. The novel, accessory, and orphan multimodular CSS identified here suggest the emergence of myxobacterial CSS and could assist in further characterizing their roles. This study is focused on chemosensory systems (CSS), which help the bacterium in directing its movement toward or away from chemical gradients. CSS are present as a single system in most of the bacteria except in some groups, including , which has 8 CSS, the highest number reported to date. This is the first comprehensive study carrying out a comparative analysis of the 22 available myxobacterial genomes, which suggests the evolutionary diversity of these systems. We are interested in understanding the distribution of CSS within all known myxobacteria and their probable evolution.

Diversity and Evolution of Myxobacterial Type IV Pilus Systems

“…These genes encode a two-component histidine kinase-response regulator pair that controls pilus expression ( Bretl et al, 2016 ). The Myxococcales are well known for having a large number of response regulators and histidine kinases compared to other bacteria ( Whitworth and Cock, 2008 ; Whitworth, 2015 ; Sharma et al, 2018 ); we noted that pilRS homologs were present in all myxobacterial genomes and outgroups organisms ( Figure 1 ). As T4P PilRS proteins are similar to other response regulators and histidine kinases present in the genome, we have shown them in Figure 1 as a single occurrence depicting the presence of a response regulator and histidine kinase above used stringent cutoffs.…”

“…No specific criteria were used to select the representative members. For representative members of order Myxococcales, we downloaded Myxococcus hansupus ( Mh : CP012109) ( Sharma et al, 2016b ), M. xanthus DK1622 ( Mx DK1622: NC_008095.1) ( Goldman et al, 2006 ), M. fulvus HW-1 ( Mf : NC_015711.1) ( Li et al, 2011 ), M. fulvus 124B02 (MfB; CP006003) ( Chen et al, 2016 ), M. stipitatus T ( Ms : NC_020126.1) ( Huntley et al, 2013 ), M. xanthus DZ2 ( Mx DZ2: AKYI00000000) ( Muller et al, 2013a ), M. xanthus DZF1 ( Mx DZF1: AOBT00000000) ( Muller et al, 2013b ), Anaeromyxobacter dehalogenans 2CP-1 ( Ad1 : NC_011891.1), Archangium gephyra DSM 2261 T ( Ag : CP011509.1) ( Sharma and Subramanian, 2017 ), Cystobacter fuscus DSM 2262 T ( Cyb : ANAH00000000) ( Sharma et al, 2018 ), Cystobacter violaceus Cb vi76 ( Cyvi : JPMI000000000) ( Stevens et al, 2014 ), Hyalangium minutum DSM 14724 T ( Hm : JMCB00000000) ( Sharma et al, 2018 ), Stigmatella aurantiaca DW4/3-1 ( Sa : NC_014623.1) ( Huntley et al, 2011 ), Corallococcus coralloides DSM 2259 T ( Cc : NC_017030.1) ( Huntley et al, 2012 ), Haliangium ochraceum SMP-2 DSM 14365 T ( Ho : NC_013440.1) ( Ivanova et al, 2010 ), Enhygromyxa salina DSM 15201 ( Es : JMCC00000000), Plesiocystis pacifica SIR-1 ( Pp : ABCS00000000), Chondromyces apiculatus DSM 436 ( Cap : ASRX00000000) ( Sharma et al, 2018 ), Chondromyces crocatus Cm c5 (Ccmc: CP012159.1) ( Zaburannyi et al, 2016 ), Sorangium cellulosum So0157-2 ( Han et al, 2013 ) ( So 0157: NC_021658.1), S. cellulosum Soce56 ( Schneiker et al, 2007 ) ( Soce 56: NC_010162.1), Labilithrix luteola DSM 27648 T ( Ll : CP012333.1), Vulgatibacter incomptus DSM 27710 T ( Vui : CP012332.1), and Sandaracinus amylolyticus DSM 53668 T ( Samy : CP011125.1) ( Sharma et al, 2016a ). Despite their origin from the same strain, we have used all three M. xanthus strains DK1622, DZ2, and DZF1 in this study ( Dey et al, 2016 ).…”

CglB adhesins secreted at bacterial focal adhesions mediate gliding motility

“…This study explored 27 myxobacterial genomes, distributed within 3 suborders and 10 families [56][57][58][59][60][61][62][63][64][65][66][67][68][69] , in addition to 58 outgroup genomes (members from 32 non-Myxococcales Deltaproteobacteria, 4 α-, 6 β-, 9 γ-, 4 £-proteobacteria, 2 Firmicutes, and 1 Actinobacteria).…”

Modulation of bacterial multicellularity via spatiotemporal polysaccharide secretion

“…Forty-order Myxococcales genomes [80][81][82][83][84][85][86][87][88][89][90][91][92][93][94][95] were downloaded from NCBI followed by RAST-based gene prediction and annotation [96]. Finally, the binary distribution (Presence/absence), location and cluster information of each cluster was mapped on the housekeeping protein-based phylogeny.…”