Abundant nitrite-oxidizing metalloenzymes in the mesopelagic zone of the tropical Pacific Ocean

Characterization of the Fe metalloproteome of a ubiquitous marine heterotroph,Pseudoalteromonas(BB2-AT2): multiple bacterioferritin copies enable significant Fe storage

“…Marine protein samples were collected and analyzed from the METZYME expedition (KM1128) in October 2011 aboard the R/V Kilo Moana and on the ProteOMZ expedition (FK160115) on the R/V Falkor using extraction and analysis methods reported previously. [51][52][53][54] While cyanobacterial functional proteins, two component regulatory systems and the nitrite oxidoreductase enzyme have been described within these metaproteomic datasets, the Pseudoalteromonas transporter described in this study has not been described. Paired metagenomic analyses were used for peptide spectra matching using the SEQUEST algorithm within Proteome Discoverer.…”

“…51 Total spectral counts are displayed without normalization approaches. 54 Map and protein section were prepared using Ocean Data View (version 5.0.0; Schlitzer, R., Ocean Data View, odv.awi.de, 2018) and the Ocean Protein Portal (https:// proteinportal.whoi.edu/). METATRYP software and marine microbial tryptic peptide database (https://metatryp.whoi.edu/) 55 was used to query the occurrence of tryptic peptides within the protein coding sequences predicted from genomes and metagenomes.…”

Genomic and kinetic analysis of novel Nitrospinae enriched by cell sorting

“…They have been found to be present in a wide range of habitats including the free water column, oxygen minimum zones (OMZs), sediments, and deep-sea trenches [5][6][7][8][9][10][11][12][13][14][15][16][17]. Interestingly, nitrite oxidoreductase (NXR), the key enzyme for nitrite oxidation, was found to be highly abundant in metaproteomic studies of OMZs [11,12] and high in situ nitrite oxidation rates were measured, although nitrite oxidation is considered to be an aerobic process and OMZs are strongly oxygen limited [5,18,19]. In addition to their importance in the nitrogen cycle, the Nitrospinae have been suggested to play a major role in dark ocean carbon fixation by contributing up to 15-45% of the fixed inorganic carbon in some environments [20].…”

Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions

“…Cells were harvested for proteomic analysis during exponential growth when [NO [41]. In addition, targeted quantitative proteomics using custom-made isotopically-labelled ( 15 N) peptide standards was performed as previously described [41]. Tryptic peptides from different proteins, including nitrite oxidoreductase (NXR), were targeted for absolute quantitation (see Table S2).…”

“…Interestingly, the N. marina genome contains genes for multiple reactions that convert the precursor cobyrinate/hydrogenobyrinate to cobalamin, and encodes all genes required for cobalamin salvage from cobinamide (Table S5). Hence, in contrast to many other bacteria that lack the complete cobalamin biosynthesis pathway [76] In addition to B vitamins, low concentrations of iron limit ocean productivity in many parts of the global ocean [80,81] and could limit NOB due to the high iron requirements of their respiratory chain [41,82]. N. marina encodes multiple metal transport systems, including a molybdenum ABC transporter module, two putative zinc transporters (ZIP family), a putative Fe 2+ /Mn 2+ transporter (VIT1/CCC1 family), two putative copper-transporting P-type ATPases, and a putative high-affinity nickel transport protein (Table S5), however, it lacks an ABC-type uptake system for Fe 3+ present in other characterized Nitrospira species [24].…”