Subcellular localization of marine bacterial alkaline phosphatases
- 15 December 2009
- journal article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences of the United States of America
- Vol. 106 (50), 21219-21223
- https://doi.org/10.1073/pnas.0907586106
Abstract
Bacterial alkaline phosphatases (APases) are important enzymes in organophosphate utilization in the ocean. The subcellular localization of APases has significant ecological implications for marine biota but is largely unknown. The extensive metagenomic sequence databases from the Global Ocean Sampling Expedition provide an opportunity to address this question. A bioinformatics pipeline was developed to identify marine bacterial APases from the metagenomic databases, and a consensus classification algorithm was designed to predict their subcellular localizations. We identified 3,733 bacterial APase sequences (including PhoA, PhoD, and PhoX) and found that cytoplasmic (41%) and extracellular (30%) APases exceed their periplasmic (17%), outer membrane (12%), and inner membrane (0.9%) counterparts. The unexpectedly high abundance of cytoplasmic APases suggests that the transport and intracellular hydrolysis of small organophosphate molecules is an important mechanism for bacterial acquisition of phosphorus (P) in the surface ocean. On average, each marine bacterium possessed at least one suite of uptake of glycerol phosphate (ugp) genes (e.g., ugpA, ugpB, ugpC, ugpE) for dissolved organic phosphorus (DOP) transport, but only half of them had ugpQ, which hydrolyzes transported DOP, indicating that cytoplasmic APases play a role in hydrolyzing transported DOP. The most abundant heterotrophic marine bacteria, alpha- and gamma-Proteobacteria, might hydrolyze DOP outside the cytoplasmic membrane, but the former could also transport and hydrolyze DOP in the cytoplasm. The abundant extracellular APases could provide bioavailable P for organisms that cannot directly access organophosphates, and thereby increase marine biological productivity and diversity.Keywords
This publication has 43 references indexed in Scilit:
- CDD: specific functional annotation with the Conserved Domain DatabaseNucleic Acids Research, 2009
- Automated high resolution ectoenzyme measurements: instrument development and deployment in three trophic regimesLimnology and Oceanography: Methods, 2007
- Meta-prediction of protein subcellular localization with reduced votingNucleic Acids Research, 2007
- The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical PacificPLoS Biology, 2007
- CAMERA: A Community Resource for MetagenomicsPLoS Biology, 2007
- MEGAN analysis of metagenomic dataGenome Research, 2007
- Total dissolved zinc in the upper water column of the subarctic North East PacificDeep Sea Research Part II: Topical Studies in Oceanography, 2002
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997
- The cyanobacterium Synechococcus sp. strain PCC 7942 contains a second alkaline phosphatase encoded by phoVMicrobiology, 1995
- Secretion of alkaline phosphatase and phsopholipase C in Pseudomonas aeruginosa is specific and does not involve an increase in outer membrane permeabilityFEMS Microbiology Letters, 1983