Abstract
Polyphosphate is a ubiquitous linear homopolymer of phosphate residues linked by high-energy bonds similar to those found in ATP. It has been associated with many processes including pathogenicity, DNA uptake and multiple stress responses across all domains. Bacteria have also been shown to use polyphosphate as a way to store phosphate when transferred from phosphate-limited to phosphate-rich media – a process exploited in wastewater treatment and other environmental contaminant remediation. Despite this, there has, to date, been little research into the role of polyphosphate in the survival of marine bacterioplankton in oligotrophic environments. The three main proteins involved in polyphosphate metabolism, Ppk1, Ppk2 and Ppx are multi-domain and have differential inter-domain and inter-gene conservation, making unbiased analysis of relative abundance in metagenomic datasets difficult. This paper describes the development of a novel Isofunctional Homolog Annotation Tool (IHAT) to detect homologs of genes with a broad range of conservation without bias of traditional expect-value cutoffs. IHAT analysis of the Global Ocean Sampling (GOS) dataset revealed that genes associated with polyphosphate metabolism are more abundant in environments where available phosphate is limited, suggesting an important role for polyphosphate metabolism in marine oligotrophs.
Highlights
Phosphate is a critical nutrient for the growth and function of cellular life, used in creation of phospholipids, nucleic acids and powering metabolism via adenosine triphosphate (ATP)
Isofunctional Homolog Annotation Tool (IHAT) analysis IHAT performs a PSI-BLAST search using a checkfile derived from a custom Hidden Markov Model (HMM) and consensus sequence created from all members associated with a particular Clustered Orthologous Group (COG) [39] within the STRING database [40] (Figure 2)
Prior to analysis of the Global Ocean Sampling (GOS) and WEC datasets, the efficacy of IHAT was tested against homolog identification using TBLASTN and HMMER3 for 11 genes chosen to cover a broad range of conservation and lengths, with known isofunctional and heterofunctional homology
Summary
Phosphate is a critical nutrient for the growth and function of cellular life, used in creation of phospholipids, nucleic acids and powering metabolism via adenosine triphosphate (ATP). The importance of phosphate in all metabolic pathways is such that it is believed to be the ultimate limiting nutrient for marine primary productivity in surface waters [1,2]. Polyphosphate is a linear homopolymer of phosphate residues linked together by high-energy phosphoanhydride bonds, similar to those found in adenosine triphosphate (ATP). It is one of the most widely distributed macromolecules and has been found in all forms of life in all three domains [12], accounting for up to 10220% of the dry weight of a cell in certain bacteria [13]. Its potential for biotechnological exploitation as an ATP substitute [15] and in remediation of environmental contaminants [16218] highlight it as a good candidate for bioengineering
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