Developing robust protein analysis profiles to identify bacterial acid phosphatases in genomes and metagenomic libraries

Abstract

Summary Phylogenetic analysis of more than 4000 annotated bacterial acid phosphatases was carried out. Our analysis enabled us to sort these enzymes into the following three types: (1) class B acid phosphatases, which were distantly related to the other types, (2) class C acid phosphatases and (3) generic acid phosphatases (GAP). Although class B phosphatases are found in a limited number of bacterial families, which include known pathogens, class C acid phosphatases and GAP proteins are found in a variety of microbes that inhabit soil, fresh water and marine environments. As part of our analysis, we developed three profiles, named Pfr‐B‐Phos, Pfr‐C‐Phos and Pfr‐GAP, to describe the three groups of acid phosphatases. These sequence‐based profiles were then used to scan genomes and metagenomes to identify a large number of formerly unknown acid phosphatases. A number of proteins in databases annotated as hypothetical proteins were also identified by these profiles as putative acid phosphatases. To validate these in silico results, we cloned genes encoding candidate acid phosphatases from genomic DNA or recovered from metagenomic libraries or genes synthesized in vitro based on protein sequences recovered from metagenomic data. Expression of a number of these genes, followed by enzymatic analysis of the proteins, further confirmed that sequence similarity searches using our profiles could successfully identify previously unknown acid phosphatases.

Shifts in the rhizobiome during consecutive in planta enrichment for phosphate‐solubilizing bacteria differentially affect maize P status

“…Elaborating on this matter, a functional metagenomics and metatranscriptomics study may be interesting for studying gene functions in the consortia. However, P‐solubilization can be mediated through a number of genes, amongst which the genes involved in inorganic P‐solubilization and organic P mineralization ( gcd , phoD , phoA , appA , phn ); non‐specific acid phosphatases (NSAPs; class A, B and C NSAP genes); P uptake and transport genes ( pst , pit ); P‐starvation response ( phoU , phoR , phoB ) (Neal et al ., 2018; Dai et al ., 2020; Udaondo et al ., 2020); PQQ biosynthetic genes (Ludueña et al ., 2017); but also (amongst others) genes involved in siderophore production, for example enterobactin ( EntD, EntF, EntC, EntE, EntB and EntA ) (Shariati et al ., 2017).…”

“…Microbial phosphate solubilization is therefore an important biostimulatory trait considering the eutrophic effects of runoff by excessive chemical P fertilizers and the declining phosphorus stocks worldwide (Cordell et al ., 2009; Bhattacharyya and Jha, 2012; Reijnders, 2014). P‐solubilizing bacteria (PSB) are able to solubilize phosphate through different mechanisms, such as the production of enzymes (phytase and phosphatase), organic acids and siderophores (Khan et al ., 2009; Sharma et al ., 2013; Pii et al ., 2015; Neal et al ., 2018; Udaondo et al ., 2020).…”

PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes

“…The high abundance of pstSCAB identified in this study was supported by the finding that the pstSCAB was a prominent transporter system for inorganic phosphorus uptake [ 67 ]. Phosphatases play a crucial role in acquiring P source from phosphoesters for microorganisms and mitigating eutrophication caused by P contamination [ 68 , 69 ]. The genes encoding the alkaline phosphates were predominant in most habitats, indicating that the mineralization potential by hydrolyzing the C-O-P bonds was the main mechanism by which microorganisms acquired orthophosphate [ 7 ].…”

The soil crisis: the need to treat as a global health problem and the pivotal role of microbes in prophylaxis and therapy

“…SOM has been proposed to promote plant growth by providing plants with small molecules (i.e. nutrients and factors required for growth), or by promoting the growth of microbes that support N mineralization, P solubilization from phytate or other sources of organic or inorganic P chemicals (Margalef et al, 2017;Udaondo et al, 2020). Therefore, the flows of C and other elements in soils are highly dynamic.…”