PMID- 32151246
OWN - NLM
STAT- MEDLINE
DCOM- 20201111
LR  - 20240328
IS  - 1471-2164 (Electronic)
IS  - 1471-2164 (Linking)
VI  - 21
IP  - 1
DP  - 2020 Mar 9
TI  - Comparative genomics analysis of c-di-GMP metabolism and regulation in 
      Microcystis aeruginosa.
PG  - 217
LID - 10.1186/s12864-020-6591-3 [doi]
LID - 217
AB  - BACKGROUND: Cyanobacteria are of special concern because they proliferate in 
      eutrophic water bodies worldwide and affect water quality. As an ancient 
      photosynthetic microorganism, cyanobacteria can survive in ecologically diverse 
      habitats because of their capacity to rapidly respond to environmental changes 
      through a web of complex signaling networks, including using second messengers to 
      regulate physiology or metabolism. A ubiquitous second messenger, 
      bis-(3',5')-cyclic-dimeric-guanosine monophosphate (c-di-GMP), has been found to 
      regulate essential behaviors in a few cyanobacteria but not Microcystis, which 
      are the most dominant species in cyanobacterial blooms. In this study, 
      comparative genomics analysis was performed to explore the genomic basis of 
      c-di-GMP signaling in Microcystis aeruginosa. RESULTS: Proteins involved in 
      c-di-GMP metabolism and regulation, such as diguanylate cyclases, 
      phosphodiesterases, and PilZ-containing proteins, were encoded in M. aeruginosa 
      genomes. However, the number of identified protein domains involved in c-di-GMP 
      signaling was not proportional to the size of M. aeruginosa genomes (4.97 Mb in 
      average). Pan-genome analysis showed that genes involved in c-di-GMP metabolism 
      and regulation are conservative in M. aeruginosa strains. Phylogenetic analysis 
      showed good congruence between the two types of phylogenetic trees based on 31 
      highly conserved protein-coding genes and sensor domain-coding genes. Propensity 
      for gene loss analysis revealed that most of genes involved in c-di-GMP signaling 
      are stable in M. aeruginosa strains. Moreover, bioinformatics and structure 
      analysis of c-di-GMP signal-related GGDEF and EAL domains revealed that they all 
      possess essential conserved amino acid residues that bind the substrate. In 
      addition, it was also found that all selected M. aeruginosa genomes encode PilZ 
      domain containing proteins. CONCLUSIONS: Comparative genomics analysis of 
      c-di-GMP metabolism and regulation in M. aeruginosa strains helped elucidating 
      the genetic basis of c-di-GMP signaling pathways in M. aeruginosa. Knowledge of 
      c-di-GMP metabolism and relevant signal regulatory processes in cyanobacteria can 
      enhance our understanding of their adaptability to various environments and 
      bloom-forming mechanism.
FAU - Chen, Meng
AU  - Chen M
AD  - Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, 
      School of Environmental Science and Engineering, Shandong University, Qingdao, 
      China.
FAU - Xu, Chun-Yang
AU  - Xu CY
AD  - Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, 
      School of Environmental Science and Engineering, Shandong University, Qingdao, 
      China.
FAU - Wang, Xu
AU  - Wang X
AD  - Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, 
      School of Environmental Science and Engineering, Shandong University, Qingdao, 
      China.
FAU - Ren, Chong-Yang
AU  - Ren CY
AD  - Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, 
      School of Environmental Science and Engineering, Shandong University, Qingdao, 
      China.
FAU - Ding, Jiao
AU  - Ding J
AD  - Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, 
      School of Environmental Science and Engineering, Shandong University, Qingdao, 
      China.
FAU - Li, Li
AU  - Li L
AD  - Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, 
      School of Environmental Science and Engineering, Shandong University, Qingdao, 
      China. lili@sdu.edu.cn.
AD  - Shandong Provincial Engineering Center on Environmental Science and Technology, 
      Jinan, China. lili@sdu.edu.cn.
LA  - eng
GR  - 21577081/Natural Science Foundation of China/
PT  - Journal Article
DEP - 20200309
PL  - England
TA  - BMC Genomics
JT  - BMC genomics
JID - 100965258
RN  - 0 (Escherichia coli Proteins)
RN  - EC 4.6.- (Phosphorus-Oxygen Lyases)
RN  - EC 4.6.1.- (diguanylate cyclase)
RN  - H2D2X058MU (Cyclic GMP)
SB  - IM
MH  - Computational Biology
MH  - Cyclic GMP/*metabolism
MH  - Escherichia coli Proteins/genetics/metabolism
MH  - Gene Expression Regulation, Bacterial/*genetics
MH  - Genomics
MH  - Microcystis/classification/genetics/*metabolism
MH  - Phosphorus-Oxygen Lyases/genetics/metabolism
MH  - Phylogeny
MH  - Protein Domains
MH  - Signal Transduction
PMC - PMC7063779
OTO - NOTNLM
OT  - C-di-GMP
OT  - Comparative genomics
OT  - EAL
OT  - GGDEF
OT  - HD-GYP
OT  - Microcystis aeruginosa
OT  - Phylogenetic analysis
OT  - PilZ
COIS- The authors declare that they have no competing interests.
EDAT- 2020/03/11 06:00
MHDA- 2020/11/12 06:00
PMCR- 2020/03/09
CRDT- 2020/03/11 06:00
PHST- 2019/09/18 00:00 [received]
PHST- 2020/02/19 00:00 [accepted]
PHST- 2020/03/11 06:00 [entrez]
PHST- 2020/03/11 06:00 [pubmed]
PHST- 2020/11/12 06:00 [medline]
PHST- 2020/03/09 00:00 [pmc-release]
AID - 10.1186/s12864-020-6591-3 [pii]
AID - 6591 [pii]
AID - 10.1186/s12864-020-6591-3 [doi]
PST - epublish
SO  - BMC Genomics. 2020 Mar 9;21(1):217. doi: 10.1186/s12864-020-6591-3.