TABLE 3

Genes unique to the Puerto Rico Trench metagenomea

Product nameCOGs category, descriptionCOGs IDBLAST result proteinb
PRT Marinosulfonomonas SAG
    Arsenite oxidase, small subunitC, energy production and conversionCOG0723Arsenite oxidase, small-subunit-domain-containing protein (Pseudovibrio sp. FO-BEG1)
    Nitrous oxide reductase apoproteinC, energy production and conversionCOG4263Nitrous oxide reductase (Ruegeria lacuscaerulensis)
    Intracellular septation protein AD, cell cycle control, cell division, chromosome partitioningCOG2917Multidrug transporter (Roseobacter sp. SK209-2-6)
    Tryptophan 2,3-dioxygenase (vermilion)E, amino acid transport and metabolismCOG3483Tryptophan 2,3-dioxygenase (Leisingera methylohalidivorans DSM 14336)
    4-Aminobutyrate aminotransferase and related aminotransferasesE, amino acid transport and metabolismCOG01604-Aminobutyrate aminotransferase (Rhizobium leguminosarum)
    ABC-type sugar transport systems, ATPase componentsG, carbohydrate transport and metabolismCOG3839ABC transporter ATP-binding protein (Roseovarius sp. strain TM1035)
    Hypothetical proteinK, transcriptionCOG2002Transcriptional regulator (“Candidatus Nitrosopumilus salaria”)
    Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domainK, transcriptionCOG2197Transcriptional regulator (Octadecabacter arcticus 238)
    3-Methyladenine DNA glycosylaseL, replication, recombination, and repairCOG2818DNA-3-methyladenine glycosylase 1 (Roseobacter litoralis Och 149)
    Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF familyO, posttranslational modification, protein turnover, chaperonesCOG1975Hypothetical protein thalar_02047 (Thalassobacter arenae DSM 19593)
    PeroxiredoxinO, posttranslational modification, protein turnover, chaperonesCOG0678Peroxiredoxin (R. litoralis Och 149)
    Hypothetical proteinR, general function prediction onlyCOG1058Molybdenum cofactor biosynthesis protein (Roseobacter sp. strain CCS2)
    Hypothetical proteinMembrane protein (Nitrosopumilus sp. strain SJ)
    Polysaccharide lyase family 8, N-terminal alpha-helical domainSilent information regulator protein Sir2 (Elizabethkingia meningoseptica)
    Hypothetical proteinSulfatase (Jannaschia sp. strain CCS1)
    Hemerythrin HHE cation binding domainLysR family HTH-type transcriptional regulator (Phaeobacter gallaeciensis 2.10)
    Hypothetical proteinMORN repeat protein (endosymbiont of Ridgeia piscesae)
PRT Psychromonas SAG
    FerredoxinC, energy production and conversionCOG0633Ferredoxin (Psychromonas sp. CNPT3)
    Phosphotransferase system fructose-specific component IIBG, carbohydrate transport and metabolismCOG1445PTS, fructose-specific IIBC component (Psychromonas sp. CNPT3)
    Hypothetical proteinN, cell motilityCOG1344Flagellin (Psychromonas sp. CNPT3)
PRT Nitrosopumilus SAG
    Hypothetical proteinC, energy production and conversionCOG3794Blue (type 1) copper domain-containing protein (“Candidatus Nitrosopumilus sp.” AR2)
    Histones H3 and H4B, chromatin structure and dynamicsCOG2036Transcription factor CBF/NF-Y/histone domain-containing protein (N. maritimus)
    Hypothetical proteinK, transcriptionCOG2002AbrB family transcriptional regulator (N. maritimus SCM1)
    Hypothetical proteinK, transcriptionTranscriptional regulator (“Candidatus Nitrosopumilus salaria”)
  • a SAG sequence reads that recruited to the Puerto Rico Trench metagenome but did not recruit to the other metagenome samples (GOS-NHRI/PCPA/FIGI/SARA [32, 33], HOT 4000 m [17], and DeepMed 3000 m [18] [see Table S1 in the supplemental material]) were identified using FR-HIT (29). The PRT SAR11 SAG did not have any genes that uniquely recruited to the PRT metagenome. HTH, helix-turn-helix; HHE, histidine-histidine-glutamate.

  • b MORN, membrane occupation and recognition nexus; PTS, phosphotransferase system; CBF, CCAAT-binding factor; NF-Y, nuclear transcription factor Y; IIBC, enzyme II B and C combined domains.