Computational prediction of the osmoregulation network in Synechococcus sp. WH8102

Mao, Xizeng; Olman, Victor; Stuart, Rhona; Paulsen, Ian T.; Palenik, Brian; Xu, Ying

doi:10.1186/1471-2164-11-291

Cited by 14 publications

(13 citation statements)

References 49 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…[ 50 ]. As discussed above, this knowledge also allows the prediction of novel producers of glycine betaine form genome sequencing projects [ 51 ] and the computational prediction of osmoregulatory networks in cyanobacteria [ 52 ].…”

Section: Compatible Solutes–universal and Usefulmentioning

confidence: 99%

Salt Acclimation of Cyanobacteria and Their Application in Biotechnology

Pade

Hagemann

2014

Life

124

View full text Add to dashboard Cite

The long evolutionary history and photo-autotrophic lifestyle of cyanobacteria has allowed them to colonize almost all photic habitats on Earth, including environments with high or fluctuating salinity. Their basal salt acclimation strategy includes two principal reactions, the active export of ions and the accumulation of compatible solutes. Cyanobacterial salt acclimation has been characterized in much detail using selected model cyanobacteria, but their salt sensing and regulatory mechanisms are less well understood. Here, we briefly review recent advances in the identification of salt acclimation processes and the essential genes/proteins involved in acclimation to high salt. This knowledge is of increasing importance because the necessary mass cultivation of cyanobacteria for future use in biotechnology will be performed in sea water. In addition, cyanobacterial salt resistance genes also can be applied to improve the salt tolerance of salt sensitive organisms, such as crop plants.

show abstract

Section: Compatible Solutes–universal and Usefulmentioning

confidence: 99%

Salt Acclimation of Cyanobacteria and Their Application in Biotechnology

Pade

Hagemann

2014

Life

124

View full text Add to dashboard Cite

show abstract

“…P. salivibrio survives in salt concentrations between 1 and 5% [ 1 ], sufficient to explain its presence in a saltern, but not tolerant in the range reached by some extreme halophiles. The P. salivibrio genome was compared to the compendium of resources for dealing with osmotic stress discussed for Synechococcus [ 44 ] and other systems as represented in the panel of representative genomes (Additional file 2 : Table S2, osmotic stress). At the most basic level, in all bacteria Na + is actively exported and K + is actively imported to balance osmotic stress.…”

Section: Resultsmentioning

confidence: 99%

Complete genome of streamlined marine actinobacterium Pontimonas salivibrio strain CL-TW6T adapted to coastal planktonic lifestyle

et al. 2018

View full text Add to dashboard Cite

BackgroundPontimonas salivibrio strain CL-TW6T (=KCCM 90105 = JCM18206) was characterized as the type strain of a new genus within the Actinobacterial family Microbacteriaceae. It was isolated from a coastal marine environment in which members of Microbactericeae have not been previously characterized.ResultsThe genome of P. salivibrio CL-TW6T was a single chromosome of 1,760,810 bp. Genomes of this small size are typically found in bacteria growing slowly in oligotrophic zones and said to be streamlined. Phylogenetic analysis showed it to represent a lineage originating in the Microbacteriaceae radiation occurring before the snowball Earth glaciations, and to have a closer relationship with some streamlined bacteria known through metagenomic data. Several genomic characteristics typical of streamlined bacteria are found: %G + C is lower than non-streamlined members of the phylum; there are a minimal number of rRNA and tRNA genes, fewer paralogs in most gene families, and only two sigma factors; there is a noticeable absence of some nonessential metabolic pathways, including polyketide synthesis and catabolism of some amino acids. There was no indication of any phage genes or plasmids, however, a system of active insertion elements was present. P. salivibrio appears to be unusual in having polyrhamnose-based cell wall oligosaccharides instead of mycolic acid or teichoic acid-based oligosaccharides. Oddly, it conducts sulfate assimilation apparently for sulfating cell wall components, but not for synthesizing amino acids. One gene family it has more of, rather than fewer of, are toxin/antitoxin systems, which are thought to down-regulate growth during nutrient deprivation or other stressful conditions.ConclusionsBecause of the relatively small number of paralogs and its relationship to the heavily characterized Mycobacterium tuberculosis, we were able to heavily annotate the genome of P. salivibrio CL-TW6T. Its streamlined status and relationship to streamlined metagenomic constructs makes it an important reference genome for study of the streamlining concept. The final evolutionary trajectory of CL-TW6 T was to adapt to growth in a non-oligotrophic coastal zone. To understand that adaptive process, we give a thorough accounting of gene content, contrasting with both oligotrophic streamlined bacteria and large genome bacteria, and distinguishing between genes derived by vertical and horizontal descent.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5019-9) contains supplementary material, which is available to authorized users.

show abstract

“…CINPER wraps the P-MAP program with an intuitive web interface, allowing a user to set the BLAST E-value cut-off (10 −6 as the default) for orthologous gene search against each organism if needed using the “Organism-specific mapping” form. For the user-specified target genome, CINPER retrieves the operon information from the DOOR operon database [17]. The mapping result consists of the initial pathway model (generally fragmented), in which all the genes are listed together and left for the user to decide if conflicts occur and how to fix them.…”

Section: Resultsmentioning

confidence: 99%

CINPER: An Interactive Web System for Pathway Prediction for Prokaryotes

Mao

Chen²,

Zhang³

et al. 2012

PLoS ONE

Self Cite

View full text Add to dashboard Cite

We present a web-based network-construction system, CINPER (CSBL INteractive Pathway BuildER), to assist a user to build a user-specified gene network for a prokaryotic organism in an intuitive manner. CINPER builds a network model based on different types of information provided by the user and stored in the system. CINPER’s prediction process has four steps: (i) collection of template networks based on (partially) known pathways of related organism(s) from the SEED or BioCyc database and the published literature; (ii) construction of an initial network model based on the template networks using the P-Map program; (iii) expansion of the initial model, based on the association information derived from operons, protein-protein interactions, co-expression modules and phylogenetic profiles; and (iv) computational validation of the predicted models based on gene expression data. To facilitate easy applications, CINPER provides an interactive visualization environment for a user to enter, search and edit relevant data and for the system to display (partial) results and prompt for additional data. Evaluation of CINPER on 17 well-studied pathways in the MetaCyc database shows that the program achieves an average recall rate of 76% and an average precision rate of 90% on the initial models; and a higher average recall rate at 87% and an average precision rate at 28% on the final models. The reduced precision rate in the final models versus the initial models reflects the reality that the final models have large numbers of novel genes that have no experimental evidences and hence are not yet collected in the MetaCyc database. To demonstrate the usefulness of this server, we have predicted an iron homeostasis gene network of Synechocystis sp. PCC6803 using the server. The predicted models along with the server can be accessed at http://csbl.bmb.uga.edu/cinper/.

show abstract

Computational prediction of the osmoregulation network in Synechococcus sp. WH8102

Cited by 14 publications

References 49 publications

Salt Acclimation of Cyanobacteria and Their Application in Biotechnology

Salt Acclimation of Cyanobacteria and Their Application in Biotechnology

Complete genome of streamlined marine actinobacterium Pontimonas salivibrio strain CL-TW6T adapted to coastal planktonic lifestyle

CINPER: An Interactive Web System for Pathway Prediction for Prokaryotes

Contact Info

Product

Resources

About