ars.els-cdn.com · web viewsupplementary information haloplanus rubicundus sp. nov., an extremely...

Supplementary information

Haloplanus rubicundus sp. nov., an extremely halophilic archaeon isolated from solar

salt

Yeon Bee Kima,b, Joon Yong Kimc, Hye Seon Songa,b, Se Hee Leea, Na-Ri Shind, Jin-Woo

Baec, Jinjong Myounge, Ki-Eun Leef, In-Tae Chaf, Jin-Kyu Rheeb*, and Seong Woon Roha*

aMicrobiology and Functionality Research Group, World Institute of Kimchi, Gwangju

61755, Republic of Korea

bDepartment of Food Science and Engineering, Ewha Womans University, Seoul 03760,

Republic of Korea

cDepartment of Biology, Kyung Hee University, Seoul 02447, Republic of Korea

dBiological Resource Center, Korea Research Institute of Bioscience and Biotechnology,

Jeollabuk-do 56212, Republic of Korea

eKorea Zoonosis Research Institute, Chonbuk National University, Jeollabuk-do 54531,

Republic of Korea.

fMicroorganism Resources Division, National Institute of Biological Resources, Incheon

22689, Republic of Korea

*Corresponding author.

E mail addresses: [email protected] (S. W. Roh), [email protected] (J. Rhee)

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Supplementary Table S1. 16S rRNA gene sequence similarities between the two novel

strains and ten related type strains in the order of high similiarity value.

Taxon Strain AccessionSimilarity (%)

1 2 3 4

Haloplanus natans DSM 17983 KE386573 98.78 98.64 98.57 98.57

Haloplanus aerogenes CGMCC 1.10124 jgi.1058094 98.44 98.44 98.50 98.50

Haloplanus vescus CGMCC 1.8712 jgi.1058054 98.30 98.16 98.10 98.10

Haloplanus salinus YGH66 JQ237126 97.77 97.91 97.84 97.84

Haloplanus litoreus GX21 HM063950 96.93 96.79 96.72 96.72

Haloplanus salinarum SP28 KX151776 96.52 96.38 96.31 96.31

Haloplanus rallus MBLA0036 KU933931 96.46 96.33 96.26 96.26

Haloplanus ruber R35 HM159597 96.02 96.16 96.09 96.09

Haloprofundus marisrubri SB9 KJ999759 91.65 91.65 91.58 91.58

Salinigranum salinum YJ-50-S2 KC918822 91.32 91.32 91.39 91.39

16S rRNA genes: 1, Haloplanus rubicundus CBA1112T rrnA; 2, Hpn. rubicundus CBA1112T

rrnB; 3, Hpn. rubicundus CBA1113 rrnA; 4, Hpn. rubicundus CBA1113 rrnB.

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Supplementary Table S2. in silico DDH (isDDH) values between CBA1112T, CBA1113,

and closely related Haloplanus strains.

Query genome Reference genome isDDH value Model confidence interval (%)

Hpn. rubicundus CBA1112T Hpn. rubicundus CBA1113 89.5 87.1‒91.5

Hpn. natans JCM 14081T 31.0 28.6‒33.5

Hpn. aerogenes JCM 16430T 28.9 26.5‒31.4

Hpn. vescus JCM 16055T 25.4 23.1‒27.9

Hpn. salinus JCM 18368T 38.6 36.1‒41.1

Hpn. rubicundus CBA1113 Hpn. natans JCM 14081T 30.9 28.5‒33.4

Hpn. aerogenes JCM 16430T 28.9 26.5‒31.4

Hpn. vescus JCM 16055T 25.5 23.2‒28.0

Hpn. salinus JCM 18368T 38.5 36.0‒41.0

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Supplementary Table S3. Strain-specific POGs annotated and classified using the KEGG database.

Strain K numberNo. ofmatched gene

Orthology description Pathway Subcategory Category

Haloplanus rubicundusCBA1112

K07213 1 ATOX1, ATX1, copZ, golB; copper chaperone Mineral absorption Digestive system Organismal Systems

K00694 1 bcsA; cellulose synthase (UDP-forming) Starch and sucrose metabolism

Carbohydrate metabolism Metabolism

Biofilm formation - Escherichia coli

Cellular community - prokaryotes

Cellular Processes

K10742 1 DNA2; DNA replication ATP-dependent helicase Dna2 DNA replication Replication and repair Genetic Information Processing

K02316 1 dnaG; DNA primase DNA replication Replication and repair Genetic Information Processing

K04043 1 dnaK, HSPA9; molecular chaperone DnaK RNA degradation Folding, sorting and degradation

Genetic Information Processing

Longevity regulating pathway - worm

Aging Organismal Systems

Tuberculosis Infectious disease: bacterial Human Diseases

K01470 1 E3.5.2.10; creatinine amidohydrolase Arginine and proline metabolism

Amino acid metabolism Metabolism

K04042 1 glmU; bifunctional UDP-N-acetylglucosamine pyrophosphorylase /Glucosamine-1-phosphate N-acetyltransferase

Amino sugar and nucleotide sugar

metabolism


K10726 1 mcm, cdc21; replicative DNA helicase Mcm DNA replication Replication and repair Genetic Information Processing

K01893 1 NARS, asnS; asparaginyl-tRNA synthetase Aminoacyl-tRNA biosynthesis

Translation Genetic Information Processing

K11936 1 pgaC, icaA; poly-beta-1,6-N-acetyl-D-glucosamine synthase Biofilm formation - Escherichia coli


Cellular Processes

K01007 1 pps, ppsA; pyruvate, water dikinase Pyruvate metabolism Carbohydrate metabolism Metabolism

Carbon fixation pathways in prokaryotes

Energy metabolism Metabolism

Methane metabolism Energy metabolism Metabolism

K01318 1 sspA; glutamyl endopeptidase Quorum sensing Cellular community - Cellular Processes

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prokaryotesK06013 1 STE24; STE24 endopeptidase Terpenoid backbone

biosynthesisMetabolism of terpenoids

and polyketidesMetabolism

K00788 1 thiE; thiamine-phosphate pyrophosphorylase Thiamine metabolism Metabolism of cofactors and vitamins

Metabolism

K03657 2 uvrD, pcrA; DNA helicase II / ATP-dependent DNA helicase PcrA Nucleotide excision repair

Replication and repair Genetic Information Processing

Mismatch repair Replication and repair Genetic Information Processing

K13525 1 VCP, CDC48; transitional endoplasmic reticulum ATPase Protein processing in endoplasmic reticulum

Folding, sorting and degradation

Genetic Information Processing

Legionellosis Infectious disease: bacterial Human Diseases

K01537 1 ATP2C; P-type Ca2+ transporter type 2C - - -

K06930 1 bat; HTH-type transcriptional regulator, bacterioopsin transcriptional activator and related proteins

- - -

K07282 1 capA, pgsA; gamma-polyglutamate biosynthesis protein CapA - - -

K10725 3 cdc6A; archaeal cell division control protein 6 - - -

K01449 1 cwlJ, sleB; N-acetylmuramoyl-L-alanine amidase - - -

K19175 1 dptH; DNA phosphorothioation-dependent restriction protein DptH - - -

K05521 1 draG; ADP-ribosyl-[dinitrogen reductase] hydrolase - - -

K00590 4 E2.1.1.113; site-specific DNA-methyltransferase (cytosine-N4-specific)

- - -

K00571 2 E2.1.1.72; site-specific DNA-methyltransferase (adenine-specific) - - -

K03687 1 GRPE; molecular chaperone GrpE - - -

K02486 1 K02486; two-component system, sensor kinase - - -

K07058 1 K07058; membrane protein - - -

K07454 1 K07454; putative restriction endonuclease - - -

5910

K07465 1 K07465; putative RecB family exonuclease - - -

K07496 1 K07496; putative transposase - - -



K10716 1 kch, trkA, mthK, pch; voltage-gated potassium channel - - -

K07448 1 mrr; restriction system protein - - -

K12287 1 mshQ; MSHA biogenesis protein MshQ - - -

K03496 1 parA, soj; chromosome partitioning protein - - -

K00344 1 qor, CRYZ; NADPH:quinone reductase - - -

K02485 1 rssB, hnr; two-component system, response regulator - - -

K03294 1 TC.APA; basic amino acid/polyamine antiporter, APA family - - -

K06957 1 tmcA; tRNA(Met) cytidine acetyltransferase - - -

K04763 1 xerD; integrase/recombinase XerD - - -

K07114 1 yfbK; Ca-activated chloride channel homolog - - -

K16263 1 yjeH; amino acid efflux transporter - - -

K16267 1 zipB; zinc and cadmium transporter - - -

K06915 2 K06915; uncharacterized protein - - -



61112





Haloplanus rubicundusCBA1113

K00128 1 ALDH; aldehyde dehydrogenase (NAD+) Glycolysis / Gluconeogenesis


Ascorbate and aldarate metabolism


Pyruvate metabolism Carbohydrate metabolism Metabolism

Fatty acid degradation Lipid metabolism Metabolism

Glycerolipid metabolism Lipid metabolism Metabolism

Valine, leucine and isoleucine degradation


Lysine degradation Amino acid metabolism Metabolism

Arginine and proline metabolism


Histidine metabolism Amino acid metabolism Metabolism

Tryptophan metabolism Amino acid metabolism Metabolism

beta-Alanine metabolism Metabolism of other amino acids

Metabolism

Insect hormone biosynthesis

Metabolism of terpenoids and polyketides

Metabolism

Limonene and pinene degradation

Metabolism of terpenoids and polyketides

Metabolism

Chloroalkane and chloroalkene degradation

Xenobiotics biodegradation and metabolism

Metabolism

K01438 1 argE; acetylornithine deacetylase Arginine biosynthesis Amino acid metabolism Metabolism

71314

K03407 1 cheA; two-component system, chemotaxis family, sensor kinase CheA

Two-component system Signal transduction Environmental Information Processing

Bacterial chemotaxis Cell motility Cellular Processes

K00390 1 cysH; phosphoadenosine phosphosulfate reductase Sulfur metabolism Energy metabolism Metabolism

K06223 2 dam; DNA adenine methylase Mismatch repair Replication and repair Genetic Information Processing

K01439 1 dapE; succinyl-diaminopimelate desuccinylase Lysine biosynthesis Amino acid metabolism Metabolism

K00558 1 DNMT1, dcm; DNA (cytosine-5)-methyltransferase 1 Cysteine and methionine metabolism


MicroRNAs in cancer Cancer: overview Human Diseases

K16937 1 doxD; thiosulfate dehydrogenase [quinone] large subunit Sulfur metabolism Energy metabolism Metabolism

K01051 1 E3.1.1.11; pectinesterase Pentose and glucuronate interconversions



K08688 1 E3.5.3.3; creatinase Arginine and proline metabolism


K18128 1 gadh; D-glyceraldehyde dehydrogenase (NADP+) Pentose phosphate pathway


K05831 1 lysK, argE; [amino group carrier protein]-lysine/ornithine hydrolase

Lysine biosynthesis Amino acid metabolism Metabolism

Arginine biosynthesis Amino acid metabolism Metabolism

K00971 1 manC, cpsB; mannose-1-phosphate guanylyltransferase Fructose and mannose metabolism


Amino sugar and nucleotide sugar

metabolism


K10726 1 mcm, cdc21; replicative DNA helicase Mcm DNA replication Replication and repair Genetic Information Processing

K00140 1 mmsA, iolA, ALDH6A1; malonate-semialdehyde dehydrogenase (acetylating)/ methylmalonate-semialdehyde dehydrogenase

Propanoate metabolism Carbohydrate metabolism Metabolism

Inositol phosphate metabolism


81516

Valine, leucine and isoleucine degradation


beta-Alanine metabolism Metabolism of other amino acids

Metabolism

K01893 1 NARS, asnS; asparaginyl-tRNA synthetase Aminoacyl-tRNA biosynthesis

Translation Genetic Information Processing

K01480 1 speB; agmatinase Arginine and proline metabolism


K01791 1 wecB; UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing) Amino sugar and nucleotide sugar

metabolism



Biofilm formation - Vibrio cholerae


Cellular Processes

K02472 1 wecC; UDP-N-acetyl-D-mannosaminuronic acid dehydrogenase Amino sugar and nucleotide sugar

metabolism



Biofilm formation - Vibrio cholerae


Cellular Processes

K16898 2 addA; ATP-dependent helicase/nuclease subunit A - - -

K16899 2 addB; ATP-dependent helicase/nuclease subunit B - - -

K06930 2 bat; HTH-type transcriptional regulator, bacterioopsin transcriptional activator and related proteins

- - -

K10725 2 cdc6A; archaeal cell division control protein 6 - - -

K19174 1 dptG; DNA phosphorothioation-dependent restriction protein DptG - - -

K00786 1 E2.4.-.-; glycosyltransferase - - -

K01274 1 E3.4.13.-; D-alanyl-D-alanine dipeptidase - - -

K07062 1 fitB; toxin FitB [EC:3.1.-.-] - - -

K07332 1 flaI-A, flaI; archaeal flagellar protein FlaI - - -

91718

K03466 1 ftsK, spoIIIE; DNA segregation ATPase FtsK/SpoIIIE, S-DNA-T family

- - -

K01138 1 K01138; uncharacterized sulfatase - - -

K07228 1 K07228; TrkA domain protein - - -

K07468 1 K07468; putative ATP-dependent DNA ligase - - -




K10716 2 kch, trkA, mthK, pch; voltage-gated potassium channel - - -

K07452 1 mcrB; 5-methylcytosine-specific restriction enzyme B - - -

K18828 1 mvpA, vapC; tRNA(fMet)-specific endonuclease VapC - - -

K01262 1 pepP; Xaa-Pro aminopeptidase - - -

K01271 1 pepQ; Xaa-Pro dipeptidase - - -

K11928 1 putP; sodium/proline symporter - - -

K06218 1 relE, stbE; mRNA interferase RelE/StbE - - -

K03546 1 sbcC, rad50; DNA repair protein SbcC/Rad50 - - -

K03529 1 smc; chromosome segregation protein - - -

K03294 1 TC.APA; basic amino acid/polyamine antiporter, APA family - - -

K03307 1 TC.SSS; solute:Na+ symporter, SSS family - - -

K03733 1 xerC; integrase/recombinase XerC - - -

101920

K04763 2 xerD; integrase/recombinase XerD - - -

K07459 1 ybjD; putative ATP-dependent endonuclease of the OLD family - - -




　 K07095 1 K07095; uncharacterized protein - - -

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Supplementary Fig. S1. Genes of strains CBA1112T (red bar) and CBA1113 (blue bar)

functionally annotated using the COG database. One-letter abbreviations for the COG

categories: D, cell cycle control, cell division, chromosome partitioning; M, cell

wall/membrane/envelope biogenesis; N, cell motility; O, post-translational modification,

protein turnover, and chaperones; T, signal transduction mechanisms; U, intracellular

trafficking, secretion, and vesicular transport; V, defense mechanisms; B, chromatin structure

and dynamics; J, translation, ribosomal structure and biogenesis; K, transcription; L,

replication, recombination, and repair; C, energy production and conversion; E, amino acid

transport and metabolism; F, nucleotide transport and metabolism; G, carbohydrate transport

and metabolism; H, coenzyme transport and metabolism; I, lipid transport and metabolism; P,

inorganic ion transport and metabolism; Q, secondary metabolites biosynthesis, transport, and

catabolism; S, function unknown.

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Supplementary Fig. S2. The functional gene annotations of strains CBA1112T (red bar) and

CBA1113 (blue bar) using the KEGG database.

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Supplementary Fig. S3. A circular phylogenetic tree based on 16S rRNA gene sequence

with environmental Haloplanus sequences. The tree was constructed using the neighbor-

joining (NJ) algorithm with bootstrap values of 1,000. Natrinema soli 3-5T was used as an

outgroup taxon.

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Supplementary Fig. S4. Functional POG annotation of six Haloplanus strains using COG

database. One-letter abbreviations for the COG categories: D, cell cycle control, cell division,

chromosome partitioning; M, cell wall/membrane/envelope biogenesis; N, cell motility; O,

post-translational modification, protein turnover, and chaperones; T, signal transduction

mechanisms; U, intracellular trafficking, secretion, and vesicular transport; V, defense

mechanisms; B, chromatin structure and dynamics; J, translation, ribosomal structure and

biogenesis; K, transcription; L, replication, recombination, and repair; C, energy production

and conversion; E, amino acid transport and metabolism; F, nucleotide transport and

metabolism; G, carbohydrate transport and metabolism; H, coenzyme transport and

metabolism; I, lipid transport and metabolism; P, inorganic ion transport and metabolism; Q,

secondary metabolites biosynthesis, transport, and catabolism; S, function unknown. Core,

accessory, and unique genes represented as blue, green, or red bars, respectively.

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Supplementary Fig. S5. Functional POG annotation of six Haloplanus strains using KEGG

database. Core, accessory, and unique genes represented as blue, green, or red bars,

respectively.

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Supplementary Fig. S6. Histograms showing unique POG distributions of strains CBA1112T

(red bar) and CBA1113 (blue bar) based on (A) COG categories and (B) KEGG pathways.

One-letter abbreviations for the COG categories: D, cell cycle control, cell division,

chromosome partitioning; M, cell wall/membrane/envelope biogenesis; O, post-translational

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modification, protein turnover, and chaperones; T, signal transduction mechanisms; V,

defense mechanisms; J, translation, ribosomal structure and biogenesis; K, transcription; L,

replication, recombination, and repair; C, energy production and conversion; E, amino acid

transport and metabolism; G, carbohydrate transport and metabolism; Q, secondary

metabolites biosynthesis, transport, and catabolism; P, inorganic ion transport and

metabolism; S, function unknown.

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Supplementary Fig. S7. The phylogenetic tree using concatenated core genes of six

Haloplanus strains. The tree was constructed using the NJ method with 1,000 bootstrap

replications.

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Supplementary Fig. S8. Two-dimensional thin-layer chromatograms of total polar lipids

extracted from strains CBA1112T (A) and CBA1113 (B). PG, Phosphatidylglycerol; PGP-Me,

phosphatidylglycerol phosphate methyl ester; PGS, phosphatidylglycerol sulfate; S-DGD-1,

sulfated mannosyl glucosyl diether; GL, unidentified glycolipid; L1–L6, unidentified lipids.

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Supplementary Fig. S9. Fragment recruitment plot of Santa Pola saltern metagenomic reads

to genomes of Haloplanus rubicundus strain CBA1112T (A, C, E, G) and CBA1113 (B, D, F,

H). Santa Pola metagenomes of 13% (A, B), 19% (C, D), 33% (E, F), and 37% (G, H)

salinities were mapped to the genomes of strain CBA1112T and CBA1113 with percent

identity on the y-axis and the hit position along the genome on the x-axis.

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