Open Access

An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3

Standards in Genomic Sciences20149:11

https://doi.org/10.1186/1944-3277-9-11

Received: 12 June 2014

Accepted: 16 June 2014

Published: 8 December 2014

The Erratum to this article has been published in Standards in Genomic Sciences 2015 10:112

Abstract

When the genome of Ruegeria pomeroyi DSS-3 was published in 2004, it represented the first sequence from a heterotrophic marine bacterium. Over the last ten years, the strain has become a valuable model for understanding the cycling of sulfur and carbon in the ocean. To ensure that this genome remains useful, we have updated 69 genes to incorporate functional annotations based on new experimental data, and improved the identification of 120 protein-coding regions based on proteomic and transcriptomic data. We review the progress made in understanding the biology of R. pomeroyi DSS-3 and list the changes made to the genome.

Keywords

Roseobacter DMSP

Introduction

Ruegeria pomeroyi DSS-3 is an important model organism in studies of the physiology and ecology of marine bacteria [1]. It is a genetically tractable strain that has been essential for elucidating bacterial roles in the marine sulfur and carbon cycles [2, 3] and the biology and genomics of the marine Roseobacter clade [4], a group that makes up 5–20% of bacteria in ocean surface waters [5, 6]. Here we update the R. pomeroyi DSS-3 genome with 189 changes collected from the work of several research groups over the last ten years.

Organism information

Ruegeria pomeroyi DSS-3 (formerly Silicibacter pomeroyi DSS-3 [7]) is a motile gram-negative alphaproteobacterium in the marine Roseobacter lineage [8]. This mesophilic, heterotrophic bacterium was isolated from an estuary in coastal Georgia, U.S.A [9] (Table 1).
Table 1

Classification and general features of Ruegeria pomeroyi DSS-3 according to MIGS recommendations[9]

MIGS ID

Property

Term

Evidence codea

 

Current classification

Domain Bacteria

TAS [10]

  

Phylum Proteobacteria

TAS [11]

  

Class Alphaproteobacteria

TAS [12, 13]

  

Order Rhodobacterales

TAS [12, 14]

  

Family Rhodobacteraceae

TAS [12, 15]

  

Genus Ruegeria

TAS [7, 1618]

  

Species Ruegeria pomeroyi

TAS [7, 19]

  

Type strain DSS-3 = ATCC 700808 T = DSM 15171

 
 

Gram stain

Negative

TAS [8]

 

Cell shape

Rod

TAS [8]

 

Motility

Motile

TAS [8]

 

Sporulation

Non-sporulating

NAS

 

Temperature range

Mesophile (10°C-40°C)

TAS [8]

 

Optimum temperature

30°C

 
 

Carbon source

Acetate, ethanol, DL-β-hydroxybutyrate, glucose, succinate, acrylic acid, cysteic acid, glycerol, citrate, pyruvate, casamino acids, L-alanine, L-arginine, L-serine, L-taurine, L-methionine, DMSP and glycine betaine

TAS [8]

 

Energy source

Carbon compounds

 
 

Terminal electron receptor

Oxygen

 

MIGS-6

Habitat

Marine

 

MIGS-6.3

Salinity

Optimum 100–400 mM

TAS [8]

MIGS-22

Oxygen

Aerobic

TAS [8]

MIGS-15

Biotic relationship

Free-living

TAS [8]

MIGS-14

Pathogenicity

Non-pathogenic

NAS

MIGS-4

Geographic location

Coastal Georgia, USA

TAS [8]

MIGS-5

Sample collection time

June 1996

NAS

MIGS-4.1 MIGS-4.2

Latitude – Longitude

31.989616 N, 81.022768 W

NAS

MIGS-4.3

Depth

Surface

NAS

MIGS-4.4

Altitude

Sea level

NAS

aEvidence codes - TAS: Traceable Author Statement (i.e., a direct report exists in the literature); NAS: Non-traceable Author Statement (i.e., not directly observed for the living, isolated sample, but based on a generally accepted property for the species, or anecdotal evidence).

Genome sequencing information

Genome project history

The genome of R. pomeroyi DSS-3 was sequenced in 2003 by The Institute for Genomic Research (now the J. Craig Venter Institute) using Sanger sequencing (Table 2), and was annotated using Glimmer 2 [20] and the TIGR Assembler [21]. The genome was published in 2004 [1].
Table 2

Project information

MIGS ID

Property

Term

MIGS-31

Finishing quality

Closed genome [1]

MIGS-28

Libraries used

1–2 kb and 12–15 kb inserts [1]

MIGS-29

Sequencing platforms

Sanger

MIGS-31.2

Fold coverage

Not reported

MIGS-30

Assemblers

The TIGR Assembler [20]

MIGS-32

Gene calling method

Glimmer 2.0 [20]

 

Genome Database release

NCBI Refseq, release version #8

 

Genbank ID

CP000031.2, CP000032.1

 

Genbank Date of Release

December 16, 2004

 

GOLD ID

Gc00242

 

Project relevance

The first heterotrophic marine bacterium sequenced

Genome properties

The R. pomeroyi DSS-3 genome contains a 4,109,437 bp circular chromosome (5 bp shorter than previously reported [1]) and a 491,611 bp circular megaplasmid, with a G + C content of 64.1 (Table 3). A detailed description of the genome is found in the original article [1].
Table 3

Genome statistics

Attribute

Value

% of totala

Genome size (bp)

4,601,048

100.0

DNA coding region (bp)

4,144,250

90.1

DNA G + C content (bp)

2,947,874

64.1

Total genesb

4371

100.0

RNA genes

64

1.5

Protein-coding genes

4276

97.8

aThe total is based on either the size of the genome in base pairs or the total number of genes in the annotated genome.

bAlso includes pseudogenes.

Reannotation

The R. pomeroyi DSS-3 genome has been instrumental in expanding knowledge of the marine sulfur cycle, particularly the role of marine bacteria in controlling the flux of volatile sulfur to the atmosphere [3, 22] and the bacterial transformations of dimethylsulfoniopropionate (DMSP) [3, 23], dimethylsulfide, and sulfonates [24, 25]. Since 2006, many of the genes mediating the uptake and metabolism of DMSP have been identified from the R. pomeroyi DSS-3 genome. These include the demethylation pathway genes dmdABCD[2, 22] and the cleavage pathway genes dddD, dddP, dddQ, dddW, acuK, acuN, dddA and dddC[23, 26, 27]. Although many genes were identified first in R. pomeroyi DSS-3, these are now known to be widespread in ocean surface waters and harbored by a number of other major marine bacterial taxa [28]. R. pomeroyi DSS-3 also transforms sulfonates and has served as a model for identifying genes required for the degradation of 2,3-dihydroxypropane-1-sufonate (hpsNOP) [29], L-cysteate (cuyARZ) [30], taurine (tauXY) and n-acetyltaurine (naaST) [24, 31, 32], 3-sulfolactate (slcD, suyAB) [29, 33] and isethionate (iseJ) [25].

Members of the marine Roseobacter lineage are capable of oxidizing sulfite and thiosulfate [34, 35], and the genome sequence of R. pomeroyi DSS-3 revealed the sox gene cluster that mediates these processes [1, 4]. Recently, the reverse dissimilatory sulfite reductase gene cluster was found in sediment-dwelling roseobacters, and homologs to the sulfite reductase genes from this pathway (soeABC) were identified in the R. pomeroyi DSS-3 genome [36]. R. Pomeroyi DSS-3 was initially studied as a member of an ecologically important bacterial taxon that appeared unusually amenable to cultivation [5], but has now played a major role in improving our understanding of global sulfur transformations.

Studies of the R. pomeroyi DSS-3 genome have also provided a better understanding of the genes involved in processing organic nitrogen compounds, such as taurine and N-acetyltaurine [24, 31, 32]. The bacterium can catabolize lysine by using the saccharopine pathway, which is used by many plants and animals, or by using the lysine dehydrogenase pathway. Under high salt conditions, it preferentially uses the latter pathway, leading to biosynthesis of the osmolyte aminoadipate. The function of several genes in both lysine pathways has recently been experimentally verified [37].

R. pomeroyi DSS-3 genome hosts at least 28 tripartite ATP-independent periplasmic (TRAP) transporters [1]. While the substrates for many of these transporters are not yet known, the TRAP transporters responsible for the uptake of 2,3-dihydroxypropane-1-sufonate (hpsKLM) [29], isethionate (iseKLM) [25], and ectoine and hydroxyectoine have been characterized (uehABC) [38, 39]. Ectoine and hydroxyectoine are used as compatible solutes by some bacteria and phytoplankton, although R. pomeroyi DSS-3 can also assimilate carbon and nitrogen from them [39]. Several genes involved in ectoine metabolism (doe, eut, ueh) have been found in the R. pomeroyi DSS-3 genome based on homology with genes in Halomonas elongata DSM 2581 T [40].

Progress has been made in understanding the mechanisms of metal uptake in R. pomeroyi DSS-3. The manganese uptake regulator mur has been experimentally validated, as have the ABC transporter genes for manganese metabolism (sitABCD) [41]. In total, 69 annotation changes were made based on new experimental data identifying genes responsible for carbon, nitrogen, sulfur, and metal uptake and metabolism [42].

Proteomics [42] and mRNA sequencing have resulted in 120 protein coding regions being identified, removed or corrected in the updated genome. A detailed proteomic study of R. pomeroyi DSS-3 under diverse growth conditions resulted in the identification of 26 novel open reading frames (ORFs) and 5 sequencing errors [42]. The function of most of the new genes is not known and 16 of the expressed polypeptides do not have known homologs. The 26 ORFs missed in the original annotation is a significant number but less than the 1% error rate predicted for Glimmer 2 [20]. The proteomic analysis was also able to correct the start sites of 64 genes [42], enhancing the information that had been obtained only from the DNA sequence [20]. Many of the ORFs identified by proteomics were independently confirmed using strand-specific messenger RNA sequences from continuous cultures [43] and the gene calling software Glimmer 3 [44]. This method also identified several genes that were originally annotated in the wrong orientation, including a novel bacterial collagen gene (SPO1999).

A list of genome updates based on these biochemical, genetic, and -omics approaches is provided in Table 4, and full details in Additional file 1: Table S1. The updated annotations have been incorporated into the official genome record at the National Center for Biotechnology Information (Bethesda, MD, USA) under accession numbers CP000031.2 and CP000032.1 and Roseobase (http://roseobase.org).
Table 4

Updates and corrections to the genome sequence

Accession

Gene locus

CDS

Gene

Type of change

YP_166946

SPO1707a

Branched-chain amino acid ABC transporter, ATP-binding protein, putative

 

Locus name

YP_167418

SPO2192a

N-formylglutamate amidohydrolase

hutG

Locus name

YP_165298

SPO0025

Hydrolase, NUDIX family

 

ORF position

YP_165304

SPO0031

ErfK/YbiS/YcfS/YnhG family protein

 

ORF position

YP_165330

SPO0056

Hypothetical protein

 

ORF position

YP_165481

SPO0212

Hypothetical protein

 

ORF position

YP_165606

SPO0343

2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase

sucB

ORF position

YP_165666

SPO0403

Conserved domain protein

 

ORF position

YP_165678

SPO0415

D-isomer specific 2-hydroxyacid dehydrogenase family protein

 

ORF position

YP_165703

SPO0440

Thioesterase family protein

 

ORF position

YP_165709

SPO0446

ABC transporter, ATP-binding protein

 

ORF position

YP_165719

SPO0456

Hypothetical protein

 

ORF position

YP_165753

SPO0491

Hypothetical protein

 

ORF position

YP_165766

SPO0504

Hypothetical protein

 

ORF position

YP_165767

SPO0505

Ribosomal protein L15

rplO

ORF position

YP_165860

SPO0600

Carboxynorspermidine decarboxylase

nspC

ORF position

YP_165899

SPO0644

Hypothetical protein

 

ORF position

YP_165937

SPO0682

Monooxygenase family protein

 

ORF position

YP_165950

SPO0695

Hypothetical protein

 

ORF position

YP_008877643

SPO0876a

Hypothetical protein

 

ORF position

YP_166130

SPO0877

Conserved domain protein

 

ORF position

YP_166199

SPO0946

Phosphomannomutase/phosphoglucomutase

algC

ORF position

YP_166255

SPO1003

ATP-dependent Clp protease, proteolytic subunit ClpP

clpP

ORF position

YP_166256

SPO1004

ATP-dependent Clp protease, ATP-binding subunit ClpX

clpX

ORF position

YP_166357

SPO1106

Hypothetical protein

 

ORF position

YP_166419

SPO1172

FMN-dependent alpha-hydroxy acid dehydrogenase family protein

 

ORF position

YP_166421

SPO1174

DNA helicase II, putative

 

ORF position

YP_166518

SPO1273

Thymidylate synthase, flavin-dependent

thyX

ORF position

YP_166577

SPO1334

Hypothetical protein

 

ORF position

YP_166601

SPO1359

Pyruvate, phosphate dikinase

ppdK

ORF position

YP_166628

SPO1386

HIT family protein

 

ORF position

YP_166803

SPO1562

Glycine cleavage system T protein, putative

 

ORF position

YP_166874

SPO1633

Hypothetical protein

 

ORF position

YP_167013

SPO1776

Pyridine nucleotide-disulphide oxidoreductase family protein

 

ORF position

YP_167049

SPO1812

Adenylate kinase

adk-2

ORF position

YP_167155

SPO1920

Tellurite resistance protein

trgB

ORF position

YP_167190

SPO1955

Glutaryl-CoA dehydrogenase

gcdH

ORF position

YP_167207

SPO1972

Nodulation protein N

 

ORF position

YP_167208

SPO1973

3-dehydroquinte dehydratase, type II

aroQ

ORF position

YP_167281

SPO2051

DNA gyrase, A subunit

gyrA

ORF position

YP_167284

SPO2054

Cytochrome c oxidase assembly protein

 

ORF position

YP_167368

SPO2141

Pyridoxamine 5''-phosphate oxidase, putative

 

ORF position

YP_167443

SPO2217

Excinuclease

 

ORF position

YP_167514

SPO2290

Hypothetical protein

 

ORF position

YP_167549

SPO2326

Hypothetical protein

 

ORF position

YP_167562

SPO2339

Enoyl-CoA hydratase/isomerase family protein

 

ORF position

YP_167570

SPO2347

Hypothetical protein

 

ORF position

YP_167571

SPO2348

Sarcosine oxidase, beta subunit family

 

ORF position

YP_167714

SPO2499

Hypothetical protein

 

ORF position

YP_167808

SPO2595

Hypothetical protein

 

ORF position

YP_167819

SPO2608

Aldehyde dehydrogenase, putative

 

ORF position

YP_167822

SPO2612

DNA-binding protein HU, putative

 

ORF position

YP_008877659

SPO2723a

Hypothetical protein

 

ORF position

YP_167934

SPO2724

Hypothetical protein

 

ORF position

YP_167992

SPO2785

NADH dehydrogense I, B subunit

nuoB

ORF position

YP_168024

SPO2816

Peptide/nickel/opine uptake family ABC transporter, permease protein

 

ORF position

YP_168061

SPO2853

Cobalt chelatase, CobS subunit

 

ORF position

YP_168080

SPO2872

Cobyrinic acid a,c-diamide synthase

cobB

ORF position

YP_168096

SPO2888

Membrane protein, putative

 

ORF position

YP_168125

SPO2917

Glutathione S-transferase family protein

 

ORF position

YP_168133

SPO2925

Sporulation related

 

ORF position

YP_168143

SPO2936

Hypothetical protein

 

ORF position

YP_168150

SPO2942

Hypothetical protein

 

ORF position

YP_168197

SPO2991

Nitroreductase family protein

 

ORF position

YP_168209

SPO3003

AMP-binding enzyme

 

ORF position

YP_168292

SPO3089

ATPase, putative

 

ORF position

YP_168317

SPO3114

Hypothetical protein

 

ORF position

YP_168354

SPO3151

HAD-superfamily subfamily IIA hydrolase, TIGR01459

 

ORF position

YP_168406

SPO3203

Guanosine-3',5'-bis(Diphosphate) 3'-pyrophosphohydrolase, putative

 

ORF position

YP_168423

SPO3220

Aminotransferase, classes I and II

 

ORF position

YP_168448

SPO3245

Nicotinate-nucleotide pyrophosphorylase

nadC

ORF position

YP_168475

SPO3278

Orotidine 5'-phosphate decarboxylase

pyrF

ORF position

YP_168540

SPO3344

Cys/Met metabolism PLP-dependent enzyme family protein

 

ORF position

YP_168563

SPO3367

Deoxyribose-phosphate aldolase

deoC

ORF position

YP_168618

SPO3422

ATP-dependent protease La domain protein

 

ORF position

YP_168712

SPO3517

Preprotein translocase, SecE subunit

secE

ORF position

YP_168722

SPO3527

Universal stress protein family protein

 

ORF position

YP_168735

SPO3540

Hypothetical protein

 

ORF position

YP_168802

SPO3607

Hypothetical protein

 

ORF position

YP_168911

SPO3717

Cytosol aminopeptidase family protein

 

ORF position

YP_168940

SPO3746

Adenine deaminse

ade

ORF position

YP_169017

SPO3829

S-formylglutathione hydrolase, putative

 

ORF position

YP_169021

SPO3833

ATP-dependent RNA helicase, DEAD/DEAH box family

 

ORF position

YP_164889

SPOA0058

Glycine cleavage system protein H

gcvH-2

ORF position

YP_165979

SPO0725

Bacterial SH3 domain family protein

 

ORF position, Function

YP_167233

SPO1999

Collagen domain protein

 

ORF position, Function

YP_008877641

SPO0561

ABC transporter

 

Sequence

YP_008877654

SPO2024

Aminotransferase

 

Sequence

YP_008877662

SPO3316a

Stress protein

 

Sequence

YP_008877661

SPO3904

Heat shock protein

 

Sequence

YP_167141

SPO1905

Fumarate hydratase, class II

fumC

Sequence, ORF position

YP_165491

SPO0222

Alanine dehydrogenase

ald

Function

YP_165503

SPO0234

Lysine dehydrogenase

lysdh

Function

YP_165504

SPO0235

α-aminoadipic-δ-semialdehyde dehydrogenase

aasadh

Function

YP_165716

SPO0453

DMSP lyase

dddW

Function

YP_165850

SPO0590

LacI family transcriptional regulator

hpsR

Function

YP_165851

SPO0591

Dihydroxypropanesulfonate (DHPS) TRAP transporter

hpsK

Function

YP_165852

SPO0592

Dihydroxypropanesulfonate (DHPS) TRAP transporter

hpsL

Function

YP_165853

SPO0593

Dihydroxypropanesulfonate (DHPS) TRAP transporter

hpsM

Function

YP_165854

SPO0594

Dihydroxypropanesulfonate-3-dehydrogenase

hpsN

Function

YP_165855

SPO0595

R or S-dihydroxypropanesulfonate-2-dehydrogenase

hpsO

Function

YP_165856

SPO0596

S or R-dihydroxypropanesulfonate-2-dehydrogenase

hpsP

Function

YP_165857

SPO0597

UspA stress protein

hpsQ

Function

YP_165858

SPO0598

Membrane-bound sulfolactate dehydrogenase

slcD

Function

YP_165912

SPO0657

Metallochaperone, putative

naaT

Function

YP_165913

SPO0658

N-acetyltaurine amidohydrolase

naaS

Function

YP_165914

SPO0659

LysR family transcriptional regulator

naaR

Function

YP_165915

SPO0660

N-acetyltaurine ABC transporter, periplasmic binding protein

naaA

Function

YP_165916

SPO0661

N-acetyltaurine ABC transporter, permease protein

naaB

Function

YP_165917

SPO0662

N-acetyltaurine ABC transporter, permease protein

naaB'

Function

YP_165918

SPO0663

N-acetyltaurine ABC transporter, ATP-binding protein

naaC

Function

YP_165919

SPO0664

N-acetyltaurine ABC transporter, ATP-binding protein

naaC'

Function

YP_165928

SPO0673

Taurine-pyruvate aminotransferase

tpa

Function

YP_165929

SPO0674

Taurine ABC transporter, periplasmic taurine-binding protein

tauA

Function

YP_165930

SPO0675

Taurine ABC transporter, ATP-binding protein

tauB

Function

YP_165931

SPO0676

Taurine ABC transporter, permease protein

tauC

Function

YP_166034

SPO0781

Phosphonate ABC transporter substrate-binding protein

phnD

Function

YP_166387

SPO1136

Diaminobutyric acid transaminase

doeD

Function

YP_166388

SPO1137

Aspartate-semialdehyde dehydrogenase

doeC

Function

YP_166389

SPO1138

AsnC/Lrp-like DNA-binding protein, transcriptional regulator

doeX

Function

YP_166390

SPO1139

Nα-acetyl-L-2,4-diaminobutyric acid deacetylase

doeB

Function

YP_166391

SPO1140

Ectoine hydrolase

doeA

Function

YP_166392

SPO1141

Ectoine utilization protein EutC

eutC

Function

YP_166394

SPO1143

Ectoine utilization protein EutA

eutA

Function

YP_166396

SPO1145

Ectoine/5-hydroxyectoine TRAP transporter, periplasmic binding protein

uehC

Function

YP_166397

SPO1146

Ectoine/5-hydroxyectoine TRAP transporter, small integral membrane protein

uehB

Function

YP_166398

SPO1147

Ectoine/5-hydroxyectoine TRAP transporter, large integral membrane protein

uehA

Function

YP_166399

SPO1148

Transcriptional regulator, GntR family

gntR

Function

YP_166792

SPO1551

Trimethylamine (TMA) monooxygenase

tmm

Function

YP_166837

SPO1596

DMSP lyase

dddQ

Function

YP_166942

SPO1703

DMSP lyase

dddD

Function

YP_167149

SPO1914

NADPH-dependent acrylyl-CoA reductase

acuI

Function

YP_167183

SPO1948

Phosphate ABC transporter substrate-binding protein

pstS

Function

YP_167275

SPO2045

3-methylmercaptopropionyl-CoA ligase

dmdB

Function

YP_167522

SPO2299

DMSP lyase

dddP

Function

YP_167578

SPO2355

Isethionate dissimilation regulator

iseR

Function

YP_167579

SPO2356

Isethionate TRAP transporter

iseM

Function

YP_167580

SPO2357

Isethionate TRAP transporter

iseL

Function

YP_167581

SPO2358

Isethionate TRAP transporter

iseK

Function

YP_167582

SPO2359

Isethionate dehydrogenase

iseJ

Function

YP_167694

SPO2477

Manganese uptake regulator

mur

Function

YP_168390

SPO3187

(2R)-3-sulfolactate dehydrogenase

comC

Function

YP_168503

SPO3307

Lysine-ketoglutarate reductase

lkr

Function

YP_168559

SPO3363

Manganese ABC transporter, permease protein

sitD

Function

YP_168560

SPO3364

Manganese ABC transporter, permease protein

sitC

Function

YP_168561

SPO3365

Manganese ABC transporter, ATP-binding protein

sitB

Function

YP_168562

SPO3366

Manganese ABC transporter, periplasmic protein

sitA

Function

YP_168752

SPO3557

Sulfite dehydrogenase subunit SoeC; transmembrane sulfate transporter

soeC

Function

YP_168753

SPO3558

Sulfite dehydrogenase iron-sulfur cluster-binding subunit SoeB; cytosolic protein

soeB

Function

YP_168754

SPO3559

Sulfite dehydrogenase molybdopterin cofactor-binding subunit SoeA; cytosolic protein

soeA

Function

YP_168755

SPO3560

Phosphate acetyltransferase

pta

Function

YP_168757

SPO3562

Taurine transcriptional regulator

tauR

Function

YP_168992

SPO3804

3-methylmercaptopropionyl-CoA dehydrogenase

dmdC

Function

YP_168993

SPO3805

Methylthioacryloyl-CoA hydratase

dmdD

Function

YP_164988

SPOA0157

Sulfite exporter

cuyZ

Function

YP_164989

SPOA0158

L-cysteate sulfo-lyase

cuyA

Function

YP_164990

SPOA0159

Transcriptional regulator cuyR

cuyR

Function

YP_165136

SPOA0309

Sulphoacetaldehyde acetyltransferase

 

Function

YP_008877636

SPO0344a

Hypothetical protein

 

New ORF

YP_008877637

SPO0346a

Hypothetical protein

 

New ORF

YP_008877638

SPO0360a

Hypothetical protein

 

New ORF

YP_008877639

SPO0491a

Hypothetical protein

 

New ORF

YP_008877640

SPO0504a

Hypothetical protein

 

New ORF

YP_008877642

SPO0628a

Hypothetical protein

 

New ORF

YP_008877644

SPO1044a

Hypothetical protein

 

New ORF

YP_008877645

SPO1094a

Hypothetical protein

 

New ORF

YP_008877646

SPO1226a

Hypothetical protein

 

New ORF

YP_008877647

SPO1252a

Transcriptional regulator

 

New ORF

YP_008877648

SPO1310a

Hypothetical protein

 

New ORF

YP_008877649

SPO1337a

Hypothetical protein

 

New ORF

YP_008877650

SPO1352a

Hypothetical protein

 

New ORF

YP_008877651

SPO1356a

Signal transduction

 

New ORF

YP_008877652

SPO1364a

Hypothetical protein

 

New ORF

YP_008877653

SPO1412a

Hypothetical protein

 

New ORF

YP_008877655

SPO2213a

Hypothetical protein

 

New ORF

YP_008877656

SPO2341a

Hypothetical protein

 

New ORF

YP_008877657

SPO2478

RNA helicase

 

New ORF

YP_008877658

SPO2652a

Polyketide cyclase

 

New ORF

YP_008877660

SPO2973a

Hypothetical protein

 

New ORF

YP_008877663

SPO3452a

Hypothetical protein

 

New ORF

YP_008877664

SPO3498a

Hypothetical protein

 

New ORF

YP_008877665

SPO3673a

Hypothetical protein

 

New ORF

AHC32567

SPOA0087a

Esterase-lipase

 

New ORF

AHC32568

SPOA0272a

Hypothetical protein

 

New ORF

YP_165305

-

Hypothetical protein

 

Removed ORF

YP_165605

-

Hypothetical protein

 

Removed ORF

YP_166669

-

Hypothetical protein

 

Removed ORF

YP_168865

-

Hypothetical protein

 

Removed ORF

YP_165238

-

Hypothetical protein

 

Removed ORF

Conclusion

Ten years after the publication of the Ruegeria pomeroyi DSS-3 genome sequence, advances in knowledge of gene function and structural genome features motivated an annotation update. As an ecologically-relevant heterotrophic marine bacterium that is amenable to laboratory studies and genetic manipulation, R. pomeroyi is serving as a valuable model organism for investigations of the ecology, biochemistry, and biogeochemistry of ocean microbes.

Notes

Declarations

Acknowledgements

This work was supported by NSF grant MCB-1158037 and the Gordon and Betty Moore Foundation. We are grateful to A. Cook and K. Denger for adopting R. pomeroyi DSS-3 in their sulfonate research, and A. Burns for reviewing the mRNA data.

Authors’ Affiliations

(1)
Department of Marine Sciences, University of Georgia

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