International Journal of Genomics

International Journal of Genomics / 2009 / Article

Research Article | Open Access

Volume 2009 |Article ID 354649 | 16 pages | https://doi.org/10.1155/2009/354649

ATP-Binding Cassette Systems of Brucella

Academic Editor: Graziano Pesole
Received16 Jun 2009
Accepted02 Dec 2009
Published11 Feb 2010

Abstract

Brucellosis is a prevalent zoonotic disease and is endemic in the Middle East, South America, and other areas of the world. In this study, complete inventories of putative functional ABC systems of five Brucella species have been compiled and compared. ABC systems of Brucella melitensis 16M, Brucella abortus 9-941, Brucella canis RM6/66, Brucella suis 1330, and Brucella ovis 63/290 were identified and aligned. High numbers of ABC systems, particularly nutrient importers, were found in all Brucella species. However, differences in the total numbers of ABC systems were identified (B. melitensis, 79; B. suis, 72; B. abortus 64; B. canis, 74; B. ovis, 59) as well as specific differences in the functional ABC systems of the Brucella species. Since B. ovis is not known to cause human brucellosis, functional ABC systems absent in the B. ovis genome may represent virulence factors in human brucellosis.

1. Introduction

Brucella species are the causative agents of brucellosis, the world’s most prevalent zoonotic disease, with high occurrences in endemic areas including the Middle East, Asia, Mexico, and the Mediterranean [1]. The bacteria are small nonmotile, Gram-negative, nonspore-forming coccobacilli that reside within the subphylum α-proteobacteria, which also includes nitrogen-fixing bacteria of the genus Nitrobacter, Rhizobium, Agrobacterium, and Rickettsia [2]. They are considered facultative intracellular pathogens.

There are six traditionally recognised Brucella species that have different host preferences: Brucella melitensis (which usually infects sheep and goats), Brucella abortus (cattle), Brucella suis (pigs), Brucella ovis (sheep), Brucella canis (dogs), and Brucella neotomae (desert wood rats). Furthermore, there are three newly identified Brucella species isolated from marine mammals: Brucella pinnipedialis (seals) [3], Brucella ceti (dolphins and porpoises) [3], and Brucella microti (voles) [4]. Although Brucella are primarily animal pathogens causing infectious abortions in females and orchitis in males [5], four of the nine species may infect humans (B. melitensis, B. abortus, B. suis, and occasionally B. canis, in order of disease severity) causing a range of flu-like symptoms including fever, sweats, malaise, and nausea [6]. Transmission to humans takes place via three recognised channels: (i) the consumption of infected animal products, (ii) direct contact with infected animal birth products, and (iii) the inhalation of aerosolised Brucella. Due to the nature of the human disease and the ability to be infectious via aerosol, Brucella species have been classified as category B threat agents by the US Centre for Disease Control and Prevention (CDC) [7].

Genome sequence analysis of B. melitensis 16M [8], B. suis 1330 [9], B. abortus 9-941 [10], B. canis RM6/66 (NCBI: NC_009504 and NC_009505, unpublished), and B. ovis 63/290 (NCBI: NC_010103 and NC_0010104, unpublished) has demonstrated the close relatedness of these organisms [11, 12]. The genomic DNA of each strain comprises two chromosomes of approximately 2.1 Mb and 1.2 Mb. DNA-DNA hybridisations between the species had previously revealed over similarity between the species, leading to the suggestion that all Brucella species should be classified as B. melitensis [13, 14]. However, it is widely believed that the differences in host specificity and pathogenicity are related to Brucella genetics; although there is currently little experimental evidence to support this, a few studies have found differences between the Brucella species genomes that may support this hypothesis [10, 15, 16]. A significant proportion of the Brucella genomes appear to code for ATP-binding cassette (ABC) systems.

ABC transporters are responsible for the import and export of many different substances across cellular membranes [17]. Although ABC transporters are extremely versatile, they all contain one defining feature, the ability to hydrolyse ATP to ADP, providing the energy needed for active transport. ABCs have three main conserved motifs known as Walker A (G-X-X-G-X-G-K-S/T, where X represents any amino acid residue), Walker B (ø-ø-ø-ø-D, where ø designates a hydrophobic residue), and a signature sequence (LSGGQ) [18]. The Walker A and Walker B motifs form tertiary structure enabling ATP-binding and can be found in all ATP-binding molecules. The signature sequence is well conserved in all ABC proteins and is also known as the linker peptide or C motif [19]. Although the configuration of ABC systems varies, the majority of ABC systems comprise of two hydrophilic ABC domains associated with two hydrophobic membrane-spanning domains (inner membrane (IM) proteins). Import systems are only found in prokaryotic organisms and contain both ABC domains and IM domains, along with extra-cytoplasmic binding proteins (BPs) designed to bind the specific allocrite of that ABC system. In Gram-negative bacteria the BPs are located in the periplasm whereas, in Gram-positive bacteria, they are anchored to the outer membrane of the cell via N-terminal lipid groups [20]. ABC systems import a diverse range of substrates into the bacterial cell including peptides [21], polyamines [22], metal ions [23], amino acids [24], iron [25], and sulphates [26]. In comparison, ABC systems involved in export functions usually contain only IM and ABC domains fused together via either the N-terminus (IM-ABC) or the C-terminus (ABC-IM), which homodimerise to create a functional system [27]. Substances exported by ABC transporters include antibiotics in both producing and resistant bacteria [28, 29], fatty acids in Gram-negative bacteria [27], and toxins [30]. In addition to transporters, many ABC proteins have roles in house-keeping functions, such as regulation of gene expression [31] and DNA repair [27, 32]. These proteins do not contain IM domains but are constituted of two fused ABC domains (ABC2) [27]. There is now increasing evidence that ABC systems can play roles in bacterial virulence [3336] and can be used as targets for vaccine development [37].

The recent sequencing of the genomes of B. melitensis 16M [8], B. abortus 9-941 [10], B. suis 1330 [9], B. ovis 63/290 (NCBI: NC_009504 and NC_009505, unpublished), and B. canis RM6/66 (NCBI: NC_010103 and NC_0010104, unpublished) has enabled the genomic comparison of different Brucella species. We report the creation and comparison of reannotated inventories of the functional ABC systems in Brucella. This improved annotation has assisted in understanding Brucella lifestyles and the identification of ABC systems that may be involved in virulence.

2. Methods

The prediction of ABC systems in sequenced bacterial genomes is based on annotation- and similarity-based homology assessment of identified or predicted ABC proteins from heterologous bacterial systems. The Artemis viewer (available from http://www.sanger.ac.uk) was used to visualise the sequenced genomes of B. melitensis 16 M, B. suis 1330, B. abortus 9-941, B. canis RM6/66, and B. ovis 63/290 [810]. Using the annotated genomes, ABC proteins were searched for using an array of related words, specifically “ATP-binding cassettes,” “binding protein”, or “outer membrane protein.” For completeness all proteins that were labelled as hypothetical or conserved hypothetical proteins were also checked. Hits from this search were compiled and then genes upstream and downstream were also checked to ensure that all genes from one system were found. After the genome searches were completed, protein sequences were aligned using the basic local alignment search tool (BlastP) against other ABC proteins using the ABC systems: Information on Sequence Structure and Evolution (ABCISSE) database [27, 38]. The ABCISSE database comprises 24000 proteins from 9500 annotated systems over 795 different organisms. Proteins searched against ABCISSE that scored a threshold -value of 10-6 were assigned to an ABC family and subfamily based on the hits from the ABCISSE database. Where searches on ABCISSE were unclear or hits for multiple families were produced, proteins were aligned using BlastP searches against the Genbank protein database. Use of this larger database increased the number of positive hits and functions that could be assigned. An ABC system was defined as a series of contiguous ORFs that shared the same family, subfamily, and substrate. A complete signal sequence (LSGGQ) was identified in the majority of the ABC proteins identified, and all of the other ABC proteins contained remnants of a complete signal sequence. Walker A and Walker B sequences were not sought during these searches.

The ABC system inventories compiled in this study include systems that contain genes with predicted frame shift mutations and premature stop codons. For example, the B. melitensis 16M gene BMEII0099 is a known pseudogene with multiple premature stop codons. However, this gene is part of an ABC system that is encoded by another four genes (BMEII0098, BMEII00101, BMEII102, and BMEII0103), all of which are predicted to be functional; the mutation in BMEII0099 might render the whole system nonfunctional or it is possible that the other four genes could create a partially functional system. Due to the inability to determine the functionality of ABC systems using bioinformatic techniques, the ABC systems where one or more components were predicted to be nonfunctional were excluded from the total ABC system numbers and functions of the ABC systems. Within the genomes of all Brucella species single components of ABC systems (mainly BP) not attached to individual systems were located. These were included in ABC system inventories and termed lone components but were not included in total functional ABC system counts.

3. Results and Discussion

The genome structures of Brucella species are very similar [10–12], and although it is widely believed that the differences in Brucella species virulence and host preferences are related to their genetic composition, there is little experimental evidence to support this belief. However, there are a few studies that have uncovered differences between the genomes [10, 15, 16]. In this study we have compared the presence of putative functional ABC systems in the genomes of B. melitensis 16M (BM), B. suis 1330 (BS), B. abortus 9-941(BS), B. canis RM6/66 (BC), and B. ovis 63/290 (BO). In the original annotations of these genomes, a uniform nomenclature was not used and functional assignment of the systems varied considerably. Here we describe a reannotation of the ABC systems of these bacterial strains, leading to new predicted functions of the systems and predictions about how the individual components combine to form functional systems. Complete inventories of the ABC systems of BM, BS, BA, BC, and BO are shown in Table 1.


NumberFamilySubfamilySubstrate/FunctionTypeB. melitensisB. abortusB.suisB. ovisB. canis

1ARTREGInvolved in gene expression regulationABC2BMEI0288BruAb11738BR1753BOV_1692BCAN_A1791

2ARTREGInvolved in gene expression regulationABC2BMEI0553BruAb11451BR1456BOV_1411BCAN_A1491

3ARTREGInvolved in gene expression regulationABC2BMEI1258BruAb10711BR0692BOV_0683BCAN_A0704

4CBYCBUCobalt importABCBMEI0635BruAb11365BR1368BOV_1324BCAN_A1395
CBYCBUCobalt importIMBMEI0637BruAb11364BR1367BOV_1323BCAN_A1394, CbiQ

5CCMPossibly heme exportIMBMEI1851BR0096, ccmCBOV_0094BCAN_A0098, ccmC
CCMPossibly heme exportIMBMEI1852BR0095, ccmBBOV_0093BCAN_A0097, ccmB
CCMPossibly heme exportABCBMEI1853BR0094, ccmABOV_0092BCAN_A0096, ccmA

6CDIInvolved in cell divisionIMBMEI0073, ftsXBruAb11971BR1996BCAN_A2042
CDIInvolved in cell divisionABCBMEI0072, ftsEBruAb11972, ftsEBR1997, ftsEBCAN_A2043, ftsE

7CLSO antigen export systemABCBMEI1416, rfbBBR0519, rfbEBOV_0523BCAN_A0531, rfbB
CLSO antigen export systemIMBMEI1415, rfbDBR0520, rfbDBOV_0524BCAN_A0532, rfbD

8DLM (ABCY)D-L-Methionine and derivatives importLPPBMEI1954

9DLM (ABCY)D-L-Methionine and derivatives importIMBMEII0336BruAb20271BRA0962BOV_A0903BCAN_B0983
DLM (ABCY)D-L-Methionine and derivatives importABCBMEII0337BruAb20272BRA0961BOV_A0902BCAN_B0982
DLM (ABCY)D-L-Methionine and derivatives importLPPBMEII0338BruAb20273BRA0960

10DPLCYDCytochrome bd biogenesis and cysteine exportIM-ABCBMEII0761, cydCBruAb20713BRA0509BOV_A0443BCAN_B0508
DPLCYDCytochrome bd biogenesis and cysteine exportIM-ABCBMEII0762, cydDBruAb20714, cydDBRA0508, cydDBOV_A0442BCAN_B0507, CydD

11DPLMDLInvolved in mitochondrial export systemsIM-ABCBMEI0323, msbABruAb11700BR1715BOV_1657BCAN_A1753

12DPLHMTInvolved in mitochondrial export systemsIM-ABCBMEI0472BruAb11533BR1545BOV_1493BCAN_A1581
DPLHMTInvolved in mitochondrial export systemsIM-ABCBMEI0471BruAb11534BR1544BOV_1494BCAN_A1582

13DPLPRTProteases, lipase, S-layer protein exportOMPBMEI1029, TolCBruAb10954BCAN_A0957

14DPLCHVBeta-(1–>2) glucan exportIM-ABCBMEI0984BruAb11004BR0998BCAN_A1015

15DPLHMTHeavy metal tolerance proteinIM-ABCBMEI1492BruAb10321BR0442BOV_0449BCAN_A0446

16DPLHMTInvolved in mitochondrial export systemsIM-ABCBMEI1743
DPLHMTInvolved in mitochondrial export systemsIM-ABCBMEI1742BOV_0198

17DPLLIPInvolved in lipid A or polysaccharide exportIM-ABCBMEII0250BruAb20990BRA1050BOV_A0988BCAN_B1071

18DRIYHIHUnknownIMBMEI0656BruAb11347BR1349BOV_1307BCAN_A1377
DRIYHIHUnknownIMBMEI0655
DRIYHIHUnknownABC2BMEI0654BruAb11348BR1350 (ABC2-IM)BOV_1308BCAN_A1378
DRIYHIHUnknownMFPBMEI0653BruAb11349BR1351BOV_1309BCAN_A1379

19DRIYHIHUnknownIMBMEII0801BruAb20757BRA0465BCAN_B0467
DRIYHIHUnknownABCBMEII0802, drrABruAb20758BRA0464BOV_A0403BCAN_B0466
DRIYHIHUnknownMFPBMEII0803BruAb20759BRA0463BOV_A0404BCAN_B0465

20DRINOSNitrous oxide reductionIMBMEII0970, nosYBruAb20902, nosYBRA0278, nosYBOV_A0254BCAN_B0280
DRINOSNitrous oxide reductionABCBMEII0971, nosFBruAb20903, nosFBRA0277, nosFBOV_A0253BCAN_B0279
DRINOSNitrous oxide reductionSSBMEII0972BruAb20904, nosDBRA0276, nosDBOV_A0252BCAN_B0278

21FAEFatty acid exportIM-ABCBMEI0520BruAb11484BR1490BCAN_A1528

22FAEFatty acid exportIM-ABCBMEII0976BruAb20908BOV_A0247BCAN_B0273

23HAABranched-chain amino acidsIMBMIE0258, LivHBruAb11771BR1790BOV_1725BCAN_A1829
HAABranched-chain amino acidsIMBMIE0259, LivMBruAb11772BR1791BOV_1724BCAN_A1828
HAABranched-chain amino acidsABCBMEI0260, braFBruAb11770BR1788BOV_1723BCAN_A1827
HAABranched-chain amino acidsABCBMEI0261, braGBruAb11769BR1789BOV_1722BCAN_A1826
HAABranched-chain amino acidsBPBMEI0263BruAb11765BR1785BOV_1720BCAN_A1823
HAABranched-chain amino acidsBPBMEI0264BruAb11767BR1782BCAN_A1820
HAABranched-chain amino acidsBPBMEI0265BOV_1719

24HAABranched-chain amino acidsBPBMEI1930BR0014BOV_0012BCAN_A0014

25HAABranched-chain amino acidsABCBMEII0065, livFBruAb20027BRA0028BOV_A0025BCAN_B0030
HAABranched-chain amino acidsABCBMEII0066, livGBruAb20028BRA0027BOV_A0024BCAN_B0029
HAABranched-chain amino acidsIMBMEII0067, livMBruAb20025BRA0026BOV_A0023BCAN_B0028
HAABranched-chain amino acidsIMBMEII0068, livHBruAb20026BRA0025BOV_A0022BCAN_B0027
HAABranched-chain amino acidsBPBMEII0069BruAb20024BRA0024BOV_A0021BCAN_B0026

26HAABranched-chain amino acidsABCBMEII0098BruAb21132BRA1197BOV_A1099BCAN_B1227
HAABranched-chain amino acidsABCBMEII0099BruAb21133BRA1196BOV_A1098BCAN_B1226
HAABranched-chain amino acidsIMBMEII0101BruAb21131BRA1194BOV_A1097BCAN_B1225
HAABranched-chain amino acidsIMBMEII0102BruAb21130BRA1195BOV_A1096BCAN_B1224
HAABranched-chain amino acidsBPBMEII0103BruAb21129BRA1193BOV_A0195BCAN_B1223

27HAABranched-chain amino acidsABCBMEII0119BruAb21111BRA1176BOV_A1079BCAN_B1207
HAABranched-chain amino acidsIM-ABCBMEII0120BruAb21112BRA1175BOV_A1078BCAN_B1206
HAABranched-chain amino acidsIMBMEII0121BruAb21110BRA1174BCAN_B1205
HAABranched-chain amino acidsBPBMEII0122BruAb21109BRA1173BOV_A1076BCAN_B1204

28HAABranched-chain amino acidsIMBMEII0340BruAb20276BRA0957BCAN_B0977
HAABranched-chain amino acidsIMBMEII0341BruAb20277BRA0956BOV_A0897BCAN_B0978
HAABranched-chain amino acidsABCBMEII0342BruAb20278BRA0955BOV_A0896BCAN_B0976
HAABranched-chain amino acidsABCBMEII0343BruAb20279BRA0954BOV_A0895BCAN_B0975
HAABranched-chain amino acidsBPBMEII0344BruAb20280BRA0953BOV_A0894BCAN_B0974

29HAABranched-chain amino acidsABCBMEII0628BruAb20574BRA0652BOV_A0613BCAN_B0652
HAABranched-chain amino acidsABCBMEII0629BruAb20575BRA0651BOV_A0614BCAN_B0651
HAABranched-chain amino acidsIMBMEII0630BruAb20577BRA0650BOV_A0611BCAN_B0649
HAABranched-chain amino acidsIMBMEII0632BruAb20576BRA0649BOV_A0612BCAN_B0650
HAABranched-chain amino acidsBPBMEII0633BruAb20578BRA0648BOV_A0610BCAN_B0648

30HAABranched-chain amino acidsBPBMEII0875BruAb20801BRA0392BCAN_B0398
HAABranched-chain amino acidsBPBMEII0868BruAb20809BRA0400BOV_A0343BCAN_B0395
HAABranched-chain amino acidsABCBMEII0874BruAb20806BRA0395BOV_A0338BCAN_B0389
HAABranched-chain amino acidsABCBMEII0873BruAb20807BRA0394BOV_A0337BCAN_B0396
HAABranched-chain amino acidsIMBruAb20808BRA0393BOV_A0336BCAN_B0397

31ISB (ABCX)Iron/sulphur centre biogenesisCYTPBMEI1040BruAb10941BR0931
ISB (ABCX)Iron/sulphur centre biogenesisCYTPBMEI1042BruAb10940BR0933
ISB (ABCX)Iron/sulphur centre biogenesisABCBMEI1041BruAb10942BR0932

32ISVHIron-siderophores, VB12 and Hemin importABCBMEI0660BruAb11342BR1344BOV_1302BCAN_A1371
ISVHIron-siderophores, VB12 and Hemin importIMBMEI0659BruAb11343BR1345BOV_1304BCAN_A1372
ISVHIron-siderophores, VB12 and Hemin importOMRBMEI0657BruAb11344BR1347BOV_1306BCAN_A1374
ISVHIron-siderophores, VB12 and Hemin importBPBMEI0658BruAb11345BR1346BOV_1305BCAN_A1373

33ISVHIron(III) dicitrate importBPBMEII0535BruAb20476BRA0756BOV_A0705BCAN_B0763
ISVHIron(III) dicitrate importIMBMEII0536, fecDBruAb20477BRA0755BOV_A0704BCAN_B0764
ISVHIron(III) dicitrate importABCBMEII0537, fecEBruAb20478BRA0754BOV_A0703BCAN_B0762

34ISVHIron(III) importABCBMEII0604BruAb20550BRA0678BOV_A0635BCAN_B0677
ISVHIron(III) importIMBMEII0605, fatCBruAb20551BRA0676BOV_A0634BCAN_B0675
ISVHIron(III) importIMBMEII0606, fatDBruAb20552BRA0677BOV_A0633BCAN_B0676
ISVHIron(III) importBPBMEII0607BruAb20553BRA0675BOV_A0632BCAN_B0674

35METZinc importIMBMEII0176, ZnuBBruAb21061, ZnuBBRA1124, ZnuBBOV_A1029BCAN_B1152
METZinc importABCBMEII0177, ZnuCBruAb21060, ZnuCBRA1123, ZnuCBOV_A1028BCAN_B1151
METZinc importBPBMEII0178, ZnuABruAb21059, ZnuABRA1122, ZnuABOV_A1027BCAN_B1150

36MKLInvolved in toluene toleranceABCBMEI0964BruAb11025BR1020BOV_0987
MKLInvolved in toluene toleranceIMBMEI0965, ttg2BBruAb1024BR1019BOV_0986
MKLInvolved in toluene toleranceSSBMEI0963, ttg2CBruAb11026BR1021BOV_0988

37MOIThiamine importABCBMEI0283, thiQBruAb11744BR1759BOV_1698BCAN_A1798
MOIThiamine importIMBMEI0284, thiPBruAb11743, thiPBR1758, thiPBOV_1696thiP, BCAN_A1797
MOIThiamine importBPBMEI0285BruAb11744, thiBBR1757, thiBBOV_1695thiB, BCAN_A1796
38MOIPutrescine importBPBMEI0411, potFBruAb11599BR1612BOV_1556BCAN_A1649
MOIPutrescine importABCBMEI0412BruAb11598BR1611BOV_1555BCAN_A1648
MOIPutrescine importIMBMEI0413BruAb11596BR1609BOV_1554BCAN_A1647
MOIPutrescine importIMBMEI0414BruAb11597BR1610BOV_1553BCAN_A1646

39MOISulphate importIMBMEI0675, cysWBruAb11328, cysW2BR1328, cysW2BOV_1288CysW, BCAN_A1353
MOISulphate importIMBMEI0674, cysTBruAb11329BR1329BOV_1289CysT, BCAN_A1354
MOISulphate importBPBMEI0673BruAb11330BR1330BOV_1290BCAN_A1355

40MOISulphate importABCBMEI1838 cysABruAb10107BR0110BOV_0107CysA, BCAN_A0113
MOISulphate importIMBMEI1839, cysWBruAb10106BR0109, cysW1BOV_0106CysW, BCAN_A0112
MOISulphate importIMBMEI1840, cystBruAb10105, cysTBR0108BOV_0105CysT, BCAN_A0111
MOISulphate importBPBMEI1841BruAb10104BR0107BOV_0104BCAN_A0110

41MOIPhosphate importABCBMEI1986, pstBBruAb12116, pstBBR2141, pstBBOV_2056BCAN_A2185, pstB
MOIPhosphate importIMBMEI1987, pstABruAb12114, pstCBR2139, pstCBOV_2055BCAN_A2184, pstA
MOIPhosphate importIMBMEI1988, pstCBruAb12115, pstABR2140BOV_2054BCAN_A2183, pstC
MOIPhosphate importBPBMEI1989BruAb12113BR2138BOV_2053BCAN_A2128

42MOIMolybdenum importABCBMEII0003, modCBruAb20090BRA0090, modCBOV_A0084BCAN_B0093, ModC
MOIMolybdenum importIMBMEII004, modBBruAb20089BRA0089, modBBOV_A0083BCAN_B0092, ModB
MOIMolybdenum importBPBMEII0005BruAb20088BRA0088, modABOV_A0082BCAN_B0091

43MOISpermidine/putrescine importABCBMEII0193, potABruAb21046BRA1107BCAN_B1129
MOISpermidine/putrescine importIMBMEII0194, potBBruAb21044BRA1106BCAN_B1128
MOISpermidine/putrescine importIMBMEII0195, potCBruAb21045BRA1105BCAN_B1127
MOISpermidine/putrescine importBPBMEII0196BruAb21043BRA1104BCAN_B1126

44MOIUnknownBPBMEII0479BruAb20422BRA0810BOV_A0760BCAN_B0824
MOIUnknownABCBMEII0481BruAb20423BRA0809BOV_A0759BCAN_B0823
MOIUnknownIMBMEII0483BruAb20424BRA0807BOV_A0758BCAN_B0822
MOIUnknownIMBMEII0484BruAb20425BRA0808BOV_A0757BCAN_B0821

45MOIIron(III) importBPBMEII0565BruAb20510BRA0720BOV_A0676BCAN_B0726
MOIIron(III) importIM2BMEII0566BruAb20511BRA0719BOV_A0675BCAN_B0274
MOIIron(III) importABCBMEII0567BruAb20512BRA0718BOV_A0674BCAN_B0725

46MOIIron(III) importABCBMEII0583BruAb20529BRA0701BOV_A0656BCAN_B0702
MOIIron(III) importBPBMEII0584BruAb20530BRA0700BOV_A0655BCAN_B0703
MOIIron(III) importIM2BMEII0585BruAb20531BRA0699BOV_A0654BCAN_B0701

47MOISpermidine/putrescine importIMBMEII0920, potCBruAb20852BRA0328BOV_A0303BCAN_B0331
MOISpermidine/putrescine importIMBMEII0921, potBBruAb20853BRA0329BOV_A0302BCAN_B0330
MOISpermidine/putrescine importABCBMEII0922, potABruAb20855BRA0327BOV_A0301BCAN_B0329
MOISpermidine/putrescine importBPBMEII0923, potDBruAb20854BRA0326BOV_A0300BCAN_B0328

48MOIIron(III) importBPBMEII1120BruAb20113BRA0115BOV_A0105BCAN_B0119
MOIIron(III) importIMBMEII1121, sufBBruAb20111BRA0114BOV_A0104BCAN_B0118
MOIIron(III) importIMBMEII1122, sufBBruAb20112BRA0113BOV_A0103BCAN_B0117
MOIIron(III) importABCBMEII1123, sufCBruAb20110BRA0112BOV_A0102BCAN_B0116

49New1UnknownIMBMEI0013BruAb12030BR2055BOV_1975BCAN_A2101
New1UnknownABCBMEI0012BruAb12031BR2056BCAN_A2102
New1UnknownBPBMEI0014
New1UnknownBPBMEI0015

50MOSRibose importABC2BMEI0391BruAB11620, rbsA-2BR1632, rbsA-2BOV_1576BCAN_A1669
MOSRibose importIMBMEI0392BruAB11619, rbsC-2BR1631, rbsC-2BOV_1575, rbsC2BCAN_A1668
MOSRibose importBPBMEI0393BruAB11618BR1630BOV_1574BCAN_A1667

51MOSRibose ImportABCBMEI0665BruAb11337BR1339BOV_1299BCAN_A1367
MOSRibose ImportIMBMEI0664BruAb11338BR1340BOV_1300BCAN_A1368
MOSRibose ImportBPBMEI0663BruAb11340BR1342BOV_1301BCAN_A1369
MOSRibose ImportBPBMEI0662BruAb11335

52MOSRibose importBPBMEI1390BruAb10566, rbsB1BR0544, rbsB1BOV_0546 rbsB1BCAN_A0557
MOSRibose importIMBMEI1391, rbsCBruAb10565, rbsC1BR0543, rbsC1BOV_0545 rbsC1BCAN_A0555
MOSRibose importABC2BMEI1392, rbsABruAb10564, rbsA1BR0542, rbsA1BOV_0544 rbsA1BCAN_A0554, rsbA

53MOSPossibly galactosideBPBMEII0083BruAb20010BRA0010BOV_A0007
MOSPossibly galactosideABC2BMEII0085, mglABruAb20009BRA0009BOV_A0006
MOSPossibly galactosideIMBMEII0086, mglCBruAb20007BRA0007BOV_A0005
MOSPossibly galactosideIMBMEII0087BruAb20008BRA0008BOV_A0004

54MOSXylose importIMBMEII0144, xylHBruAb21089, xylHBRA1152, xylHBOV_A1057BCAN_B1181
MOSXylose importABC2BMEII0145, xylGBruAb21088, xylGBRA1151, xylGBOV_A1056BCAN_B1180, xylG
MOSXylose importBPBMEII0146, xylFBruAb21087, xylFBRA1150, xylFBOV_A1055BCAN_B1179, xylF

55MOSRibose importABC2BMEII0300, rbsABruAb20239rbsA4BRA0995, rbsA4BOV_A0937BCAN_B1014
MOSRibose importIMBMEII0301 rbsCBruAb20240,rbsC5BRA0993, rbsC5BCAN_B1013
MOSRibose importIMBMEII0302 rbsCBruAb20239, rbsC4BRA0994, rbsC5BOV_A0935BCAN_B1012
MOSRibose importBPBruAb20238BRA0996, rbsB3BOV_A0938BCAN_B1015

56MOSMonosaccharide importBPBMEII0360, chvEBruAb20296BRA0937BOV_A0879BCAN_B0957
MOSMonosaccharide importABC2BMEII0361BruAb20297BRA0936BOV_A0878BCAN_B0956
MOSMonosaccharide importIMBMEII0362BruAb20298BRA0935BOV_A0877BCAN_B0955

57MOSErythritol importABC2BMEII0432, rbsABruAb20371, rbsA3BRA0860, rbsA3BOV_A0807, rsbA3BCAN_B0877
MOSErythritol importIMBMEII0433, rbsCBruAb20372, rbsC3BRA0859, rbsC3BCAN_B0876
MOSErythritol importBPBMEII0435BruAb20373, rbsB2BRA0858, rbsB2BOV_A0805BCAN_B0875

58MOSGalactoside/Ribose importABC2BMEII0698BruAb20654BRA0570BOV_A0533BCAN_B0570
MOSGalactoside/Ribose importIMBOV_A0534BCAN_B0567
MOSGalactoside/Ribose importIMBMEII0700BruAb20655BRA0568BOV_A0535
MOSGalactoside/Ribose importIMBMEII0701BruAb20656BRA0569BCAN_B0568
MOSGalactoside/Ribose importBPBMEII0702BRA0567BOV_A0532BCAN_B0567

59MOSMonosaccharide importIMBMEII0981BruAb20913BRA0267BOV_A0242BCAN_B0268
MOSMonosaccharide importABC2BMEII0982BruAb20914BRA0266BOV_A0241BCAN_B0267
MOSMonosaccharide importBPBMEII0983BruAb20916BRA0265BOV_A0240BCAN_B0266

60o228UnknownIMBMEI0361
O228UnknownMFPBMEI0359
o228UnknownABCBMEI0360

61o228UnknownIMBruAb10085BR0087BOV_0085
O228UnknownMFPBCAN_A1712
o228UnknownABCBruAb10084BR0086BOV_0084BCAN_A1711

62o228UnknownMFPBruA11658BR1671BOV_1617
o228UnknownIM-ABCBruA11657BR1670BOV_1616BCAN_A0087

63o228Lipoprotein release systemABCBMEI1138, LolDBruAb10838,LolDBR0824, LolDBOV_0818BCAN_A0839
o228Lipoprotein release systemIMBMEI1139, LolEBruAb10837, LolEBR0823, LolEBOV_0817BCAN_A0838

64OPNDipeptide importABCBMEI0438, dppFBruAb11569BR1582BOV_1527BCAN_A1617
OPNDipeptide importABCBMEI0437, dppDBruAb11570BR1583BOV_1528BCAN_A1618
OPNDipeptide importIMBMEI0435, dppCBruAb11571BR1584BOV_1530BCAN_A1620
OPNDipeptide importIMBMEI0436, dppCBruAb11572BR1585BOV_1529BCAN_A1619
OPNDipeptide importBPBMEI0433, dppABruAb11573BR1586BOV_1531BCAN_A1621

65OPNOligopeptide importABC2BMEI1938, oppDBruAb10006BR0006BOV_0006BCAN_A0006
OPNOligopeptide importBPBMEI1934BruAb10007BR0007BOV_0009BCAN_A0010
OPNOligopeptide importBPBMEI1935BruAb10008BR0008BOV_0010BCAN_A0009
OPNOligopeptide importIMBMEI1936, oppBBruAb10009BR0009BOV_0008BCAN_A0008
OPNOligopeptide importIMBMEI1937, oppCBruAb10010BR0010BOV_0007BCAN_A0007

66OPNOligopeptide importABCBMEII0199, oppFBruAb21039BRA1100
OPNOligopeptide importABCBMEII0200, oppDBruAb21040BRA1101BCAN_B1123
OPNOligopeptide importIMBMEII0201, oppCBruAb21037BRA0099BCAN_B1122
OPNOligopeptide importIMBMEII0202, oppBBruAb21038BRA0098BCAN_B1121
OPNOligopeptide importBPBMEII01203BruAb21036BRA0097BCAN_B1119

67OPNDipeptide importABCBMEII0205, dppFBruAb21033BRA1095BOV_A0950BCAN_B1117
OPNDipeptide importABCBMEII0206, dppDBruAb21034BRA1094BOV_A0951BCAN_B1116
OPNDipeptide importIMBMEII0207, dppCBruAb21031BRA1093BCAN_B1115, dppC
OPNDipeptide importIMBruAb21032BRA1092BOV_A0952
OPNDipeptide importIMBMEII0209, dppBBOV_A0953BCAN_B1114
OPNDipeptide importBPBMEII0210BruAb21030BRA1090BOV_A0954BCAN_B1113

68OPNDipeptide/ Oligopeptide importBPBMEII0217BruAb21024BRA1084BCAN_B1107
OPNDipeptide/ Oligopeptide importIMBMEII0220BruAb21020BRA1081BCAN_B1104
OPNDipeptide/ Oligopeptide importIMBMEII0221BruAb21021BRA1080BCAN_B1103
OPNDipeptide/ Oligopeptide importABCBMEII0222BruAb21018BRA1079BCAN_B1102
OPNDipeptide/ Oligopeptide importABCBMEII0223BruAb21019BRA1078BCAN_B1101

69OPNDipeptide importBPBMEII0284BruAb20952BRA1012BOV_A0504BCAN_B1032
OPNDipeptide importIMBMEII0285BruAb20950BRA1009BOV_A0501BCAN_B1031
OPNDipeptide importIMBMEII0286BruAb20951BRA1008BOV_A0502BCAN_B1030
OPNDipeptide importABCBMEII0287BruAb20948BRA1011BOV_A0500BCAN_B1029
OPNDipeptide importABCBMEII0288BruAb20949BRA1010BOV_A0501BCAN_B1028

70OPNNickel importBPBMEII0487BruAb20428BRA0804BOV_A0754BCAN_B0818, NikA
OPNNickel importIMBMEII0488, nikBBruAb20429, nikBBRA0802, nikCBOV_A0752BCAN_B0817, NikB
OPNNickel importIMBMEII0489, nikCBruAb20430, nikVBRA0803, nikBBOV_A0753BCAN_B0816, NikC
OPNNickel importABCBMEII0490, nikDBruAb20431, nikDBRA0800, nikEBOV_A0751BCAN_B0815, NikD
OPNNickel importABCBMEII0491, nikEBruAb20432, nikEBRA0801, nikDBCAN_B0814, NikE

71OPNOligopeptide importBPBMEII0504BruAb20446BRA0783BOV_A0737BCAN_B0800
OPNOligopeptide importIMBMEII0505BruAb20447BRA0788BOV_A0736BCAN_B0799
OPNOligopeptide importIMBMEII0506BruAb20448BRA0787BOV_A0735BCAN_B0798
OPNOligopeptide importABCBMEII0507BruAb20449BRA0786BOV_A0734BCAN_B0797
OPNOligopeptide importABCBMEII0508BOV_A0733BCAN_B0796

72OPNOligopeptide importBPBMEII0691BruAb20648BRA0576BOV_A0542

73OPNOligopeptide importBPBMEII0734BruAb20684BRA0538BOV_A0468BCAN_B0538
OPNOligopeptide importBPBMEII0735, oppABruAb20685BRA0537BOV_A0467BCAN_B0537
OPNOligopeptide importIMBMEII0736BruAb20686BRA0536BOV_A0466BCAN_B0535
OPNOligopeptide importIMBMEII0737BruAb20687BRA0535BOV_A0465BCAN_B0536
OPNOligopeptide importABC2BMEII0738BruAb20688BRA0534BOV_A0464BCAN_B0534

74OPNOligopeptide importBPBMEII0859BruAb20792BRA0409BOV_A0352BCAN_B0412
OPNOligopeptide importIMBMEII0860BRA0408BOV_A0351BCAN_B0411
OPNOligopeptide importIMBMEII0861BruAb20794BRA0407BOV_A0350BCAN_B0410
OPNOligopeptide importABCBMEII0863BruAb20796BRA0405BOV_A0347BCAN_B0408
OPNOligopeptide importABCBMEII0864BruAb20797BRA0404BOV_A0348BCAN_B0407

75OSPMaltose importABCBMEI1713, malKBruAb10233BR0238BOV_0231BCAN_A0241
OSPMaltose importIMBMEI1714, malGBruAb10231BR0237BOV_0230BCAN_A0240
OSPMaltose importIMBMEI1715, malFBruAb10232BR0236BOV_0229BCAN_A0239
OSPMaltose importBPBMEI1716BruAb10230BR0235BOV_0228BCAN_A0238

76OSPOligosaccharide or polyol importABCBMEII0112, ugpCBruAb21119BRA1183BOV_A1086BCAN_B1214
OSPOligosaccharide or polyol importIMBMEII0113, ugpABruAb21118BRA1181BOV_A1085BCAN_B1213
OSPOligosaccharide or polyol importIMBMEII0114, ugpEBruAb21117BRA1182BOV_A1084BCAN_B1212
OSPOligosaccharide or polyol importBPBMEII0115BruAb21116BRA1180BCAN_B1211
77OSPOligosaccharide or polyol importIMBMEII0541BruAb20483BRA0749BOV_A0700BCAN_B0757
OSPOligosaccharide or polyol importIMBruAb20482BRA0750BOV_A0699BCAN_B0756
OSPOligosaccharide or polyol importBPBMEII0542BruAb20484BRA0748BOV_A0698BCAN_B0755
OSPOligosaccharide or polyol importABCBMEII0544BruAb20487BRA0745BOV_A0696BCAN_B0753

78OSPOligosaccharide or polyol importBPBMEII0590BruAb20537BRA0693BOV_A0648BCAN_B0691
OSPOligosaccharide or polyol importIMBMEII0591BruAb20538BRA0691BOV_A0647BCAN_B0690
OSPOligosaccharide or polyol importIMBMEII0592BruAb20539BRA0692BOV_A0646BCAN_B0689
OSPOligosaccharide or polyol importABCBMEII0593BruAb20540BRA0690BOV_A0645BCAN_B0688

79OSPSN-glycerol-3-phosphate importABCBMEII0621, ugpCBruAb20568, ugpCBRA0658, ugpCBOV_A0620BCAN_B0658
OSPSN-glycerol-3-phosphate importIMBMEII0622, ugpEBruAb20569, ugpEBRA0657, ugpEBOV_A0619BCAN_B0657
OSPSN-glycerol-3-phosphate importIMBMEII0623, ugpEBruAb20570, ugpABRA0656, ugpABOV_A0618BCAN_B0656
OSPSN-glycerol-3-phosphate importIMBMEII0624, ugpA
OSPSN-glycerol-3-phosphate importBPBMEII0625BruAb20571, ugpBBRA0655, ugpABOV_A0617BCAN_B0655

80OSPOligosaccharide or polyol importABCBMEII0750BruAb20702BRA0521BOV_A0454BCAN_B0520
OSPOligosaccharide or polyol importIMBMEII0752BruAb20704BRA0519BOV_A0452BCAN_B0518
OSPOligosaccharide or polyol importIMBMEII0753BruAb20705BRA0518BOV_A0451BCAN_B0517
OSPOligosaccharide or polyol importBPBMEII0754BruAb20706BRA0516BOV_A0449BCAN_B0516
OSPOligosaccharide or polyol importBPBMEII0755

81OSPMaltose importABCBMEII0940BruAb20874BRA0307BOV_A0282BCAN_B0308
OSPMaltose importIMBMEII0942BruAb20875BRA0306BOV_A0281BCAN_B0307
OSPMaltose importIMBMEII0943BruAb20876BRA0305BOV_A0280BCAN_B0306
OSPMaltose importBPBMEII0944BOV_A0279
OSPMaltose importBPBMEII0945BruAb20877BRA0304BCAN_B0305

82OTCNGlycine betaine/L-proline importABCBMEI0439, proVBruAb11568BR1581BOV_1526BCAN_A1616
OTCNGlycine betaine/L-proline importIMBMEI0440, proWBruAb11567BR1580BOV_1525BCAN_A1615
OTCNGlycine betaine/L-proline importBPBMEI0441, proXBruAb11566BR1579BOV_1524BCAN_A1614

83OTCNCholine SS-dependent regulation of yehZYXW BPBMEI1725BruAb10220BR0225BOV_0216BCAN_A0228
OTCNCholine SS-dependent regulation of yehZYXW IMBMEI1726, proWBruAb10217BR1222BOV_0215BCAN_A0227
OTCNCholine SS-dependent regulation of yehZYXW IMBMEI1728, proWBruAb10219BR0224BOV_0213BCAN_A0225
OTCNCholine SS-dependent regulation of yehZYXW ABCBMEI1727, proVBruAb10218BR0223BOV_0214BCAN_A0226

84OTCNOsmoprotectants, Taurine, Cyanante & NitrateBPBMEI1737BruAb10207BR0211BOV_0204BCAN_A0215
OTCNOsmoprotectants, Taurine, Cyanante & NitrateIMBMEI1739BruAb10206BR0213BOV_0202BCAN_A0213
OTCNOsmoprotectants, Taurine, Cyanante & NitrateABCBruAb10208

85OTCNTaurine importBPBMEII0109BruAb21122BRA1186BOV_A1089BCAN_B1218
OTCNTaurine importIMBMEII0107, tauCBruAb21124BRA1188BOV_A1091BCAN_B1219
OTCNTaurine importABCBMEII0108, tauBBruAb21123BRA1187BOV_A1090BCAN_B1217

86OTCNGlycine betaine/L-proline importABCBMEII0548BruAb20492BRA0740BOV_A0692BCAN_B0748
OTCNGlycine betaine/L-proline importIMBMEII0549BruAb20493BRA0739BOV_A0691BCAN_B0747
OTCNGlycine betaine/L-proline importBPBMEII0550BruAb20494BRA0738BOV_A0690BCAN_B0746

87OTCNNitrate importBPBMEII0797BruAb20753BRA0469BOV_A0406BCAN_B0471
OTCNNitrate importABCBMEII0798, nrtCBruAb20755BRA0467BOV_A0407BCAN_B0470
OTCNNitrate importIMBMEII0799, nrtBBruAb20755BRA0468BOV_A0408BCAN_B0469

88OTCNTaurine importABCBMEII0961BruAb10894BRA0286BOV_A0262BCAN_B0288
OTCNTaurine importIMBMEII0962BruAb10895BRA0285BOV_A0261BCAN_B0287
OTCNTaurine importBPBMEII0963BruAb10896BRA0284BOV_A0260BCAN_B0286

89PAOPolar amino acid importABCBMEI0108BruAb11932BR1959BOV_A0336BCAN_A2004
PAOPolar amino acid importABCBMEI0111BruAb11935BR1956BOV_1885BCAN_A2001
PAOPolar amino acid importIMBMEI0112BruAb11931BR1955BOV_1882BCAN_A2000
PAOPolar amino acid importIMBMEI0113BruAb11930BR1954BOV_1081BCAN_A1999
PAOPolar amino acid importBPBMEI0114BruAb11929BR1953BOV_1880BCAN_A1998
PAOPolar amino acid importBPBOV_1879

90PAOArginine/Ornithine biding protein precursorBPBruAb20594BOV_A0594
PAOArginine/Ornithine biding protein precursorBPBMEI1022BruAb20595BRA0632BOV_A0593
PAOArginine/Ornithine biding protein precursorBPBruAb10874BRA0631BOV_0945BCAN_A0967

91PAOGeneral L-amino acid importABCBMEI1208, appPBruAb10762BR0745BOV_A0890BCAN_A0760
PAOGeneral L-amino acid importIMBMEI1209, appMBruAb10758BR0744BOV_0739BCAN_A0759
PAOGeneral L-amino acid importIMBMEI1210, appQBruAb10760BR0743BOV_0737BCAN_A0758
PAOGeneral L-amino acid importBPBMEI1211, appJBruAb10761BR0741BOV_0738BCAN_A0756
PAOGeneral L-amino acid importBPBMEII0349, appJBruAb20285BRA0948BOV_0736BCAN_B0969

92PAOArginineBPBMEI1627BruAb10321BR0295BOV_0308

93PAOCystine importABCBMEII0599BruAb20545BRA0684BOV_A0640BCAN_B0682
PAOCystine importIMBMEII0600BruAb20546BRA0683BOV_A0639BCAN_B0681
PAOCystine importBPBMEII0601BruAb20547, fliYBRA0682, fliYBOV_A0638, fliYBCAN_B0680

94PAOPolar amino acid importIMBR0952BCAN_A0964
PAOPolar amino acid importIMBR0953BCAN_A0965
PAOPolar amino acid importBPBMEI1104BR0955BOV_0854

95PAOPolar amino acid importBPBR0862BOV_A0903

96UVRDNA repairABC2BMEI0878BruAb1110, UvrAUvrABOV_1063BCAN_A1124
97YHBGPossible LPS transport to outer membraneABCBMEI1790BruAb10153BR157BOV_0152BCAN_A0162
YHBGPossible LPS transport to outer membraneSSBMEI1791BruAb10152BR156BOV_0151BCAN_A0161

ABC: ATP-Binding Cassette; IM: Inner membrane protein; BP: Binding protein; IM-ABC: Inner membrane protein-ATP binding cassette fusion; ABC2: 2 ABC proteins fused together; OMP: Outer membrane protein; MFP: Membrane fusion protein; SS: Signal sequence; LPP: Extracytoplasmic protein with a lipoprotein type signal sequence; BM: Brucella melitensis; BA: Brucella abortus; BS: Brucella suis; Bold Text: Indicates a frame shift mutation or premature stop codon in these genes.

The Brucella strains investigated in this study all have approximately 3.3 Mb genomes comprising two chromosomes of approximately 2.1 Mb and 1.2 Mb. The total number of predicted functional ABC systems encoded by the genomes of the Brucella strains is similar but does show some variability (BM = 79, BS = 72, BA = 64, BC = 74, BO = 59). Our evaluation of the Brucella genomes confirms that these species encode a relatively high proportion of ABC system genes when compared to other bacteria [39], with an average of 8.8% of their genomes dedicated to predicted functional ABC system genes (if lone components and mutated genes are included this figure increases to 9.3%). This may reflect their relatedness to environmental -proteobacteria such as Nitrobacter and Agrobacterium which also encode high numbers of ABC systems [39] that may assist in their survival in diverse conditions.

This work reports the first full inventories of ABC systems within five genome-sequenced Brucella strains. There are a number of specific ABC systems/genes that have previously been identified in the published literature. For example, Paulsen et al. describe two ABC systems that are present in B. suis and absent in B. melitensis. The first of these is an ABC importer encoded by BR0952 (IM), BR0953 (IM), and BR0955 (BP) [9]. Although this particular system is listed in the inventory, the ABC protein component of the system was not located in the BS genome and so this system was deemed incomplete and unlikely to be functional. The system was almost completely missing from the BM genome which is consistent with the findings of Paulsen et al. [9]. The second reported system is encoded by BRA0630, BRA0631, BRA0632, BRA0633, BRA0634, and BRA0635. However, when these genes were assessed using ABCISSE, only two of the five genes were predicted to be ABC transporter binding proteins (BRA0631 and BRA0632) and no other ABC components were located. Thus we deem this system also likely to be nonfunctional. Other genes that have been identified in the literature are BRA1080 (a dipeptide ABC transporter protein indentified in BS), BMEI1742 (a mitochondrial export ABC transporter identified in BM), and BRA0749-BRA0750 (involved in oligopeptide import) [10], all of which are present in our inventories.

4. ABC System Functions

In this study, we have classified the ABC systems of BM, BS, BA, BC, and BO into classes, families, and subfamilies according to the functional classification system described by Dassa and Bouige [27] (Table 2). The Brucella strains encode 8–12 class 1 systems, characterised by an ABC-IM domain fusion and comprising predicted export systems, and 5 class 2 systems, characterised by a duplicated fused ABC and with predicted functions in antibiotic resistance and house-keeping functions. However, we have found that most of the ABC systems of Brucella species belong to class 3 with roles predicted in import processes. The further classification of Brucella ABC systems into families and subfamilies shows that there are a high number of ABC systems of specific importer families, particularly the MOI (minerals and organic ions), MOS (monosaccharide), OPN (oligopeptides and nickel), OSP (oligosaccharides and polyols), and OTCN (osmoprotectants taurine cyanate and nitrate) families, all of which primarily function to acquire nutrients.


NameDescription and Function
FamilySubfamily

Exporters (predicted and experimental)

DPL, Drugs, Peptides, HMTMitochondrial and bacterial transporters II
LipidsCHVBeta(1–2) Glucan export
MDLMitochondrial and bacterial transporters I
LIPLipid A or glycerophospholipid export
PRTProteases, Lipases, S-Layer protein export
CYDCytochrome bd biogenesis
CCMCytochrome C biogenesis
CLSCapsular polysaccharide, lipopolysaccharide and teichoic acids
FAEFatty Acid Export

Importers

DLMD- L-Methionine and derivatives
CBYCBUCobalt uptake, putative
MKLRelated to MOI family but unknown substrate
YHBGRelated to HAA family, but unknown substrate
CDICell division
METMetals
MOSMonosaccharides
MOIMineral and Organic ions
PAOPolar amino acids and Opines
HAAHydrophobic amino acids and amides
OSPOligosaccharides and polyols
OPNOligopeptides and Nickel
OTCNOsmoprotectants Taurine Cyanate and Nitrate
ISVHIron-Siderophores VitaminB-12 and Hemin

cellular process (experimental)

ISBIron-sulphur centre biogenesis
ART, Antibiotic resistance and translation regulation REGTranslation regulation
UVRDNA repair and drug resistance

Unknown

DRI, Drug resistance, bacteriocin, and lantibiotic immunity YHIHDrug resistance, putative
NOSPossible nitrous oxide reduction
NOUnclassified Systems
o228Unknown

The predicted functionality of the ABC systems within the Brucella genomes is dominated by ABC systems involved in the import of nutrients (Figure 1), and although this is not uncommon amongst bacteria, it is probable that Brucella species utilise ABC transporters to provide most of the nutrients they require [8, 39]. In support of the findings of Paulsen et al. [9], the 2.1 Mb chromosome encodes a large proportion of the ABC systems involved in molecular export and cellular process whereas the ABC systems located on the smaller chromosome are largely biased toward nutrient acquisition, leading to the idea that this second chromosome is important in the acquisition and processing of nutrients in Brucella.

Since the ABC systems were identified by homology searches, it is possible to assign each ABC importer with a predicted substrate that it imports, providing an overview of the ABC system-based import ability of the Brucella species. Table 3 shows the range of predicted substrates imported via ABC transporters within the Brucella genomes. Overall, our results show that there is little difference in the import ability between strains of the four species of Brucella that are pathogenic to humans (BM, BS, BA, and BC). However, BO lacks the ability to import 8 of the 26 listed nutrients via ABC systems. In fact, all of the 29 pseudogenes that are present within the BO ABC system inventory occur within nutrient importers. The nutrients that BO appears to be unable to import using ABC systems include polyamines (specifically spermidine and putrescine), nickel, thiamine, glycine betaine, erythritol, xylose, and molybdenum. It is possible that the defective uptake of one or more of these substrates by B. ovis may contribute to its likely lack of virulence in humans. For example, polyamines have recently been associated with bacterial virulence and pathogenicity in human pathogens [40] and polyamine transporters have therefore been targeted as novel vaccine candidate targets for human pathogens [41, 42].


SubstrateB. melitensisB. abortusB. suisB. ovisB. canis

Branch chain amino acids***************
Iron (III)********************
Cobalt****
Zinc*****
Thiamine****
Putrescine*********
Sulphate**********
Phosphate*****
Molybdenum****
Spermidine******
Ribose***************
Galactoside*******
Xylose****
Erythritol****
Dipeptides***********
Oligopeptides******************
Nickel***
Maltose*****
Oligosaccharide or polyol***********
SN-glycerol-3-phosphate****
Taurine*************
Glycine betaine***
Nitrate*****
Polar amino acids**
Cystine*****
General L amino acids****

This table does not include any ABC system with pseudogenes present. ****>5 functional systems, ***3 or 4 functional systems, **2 functional systems, *1 functional system, — No functional systems.

Two predicted erythritol transport systems have been reported that have yet to be confirmed by experimental data [8, 43]. Although the erythritol transporter identified in this study has also been identified by Crasta et al. [43], it should be noted that B. abortus S19 has this transport system inactivated by pseudogenes and yet it is still able to incorporate erythritol [43], indicating that this ABC system might not be wholly responsible for erythritol transport. Another study has demonstrated that B. ovis does not utilise erythritol as readily as other sugars [44].

In this study we have identified one ABC system in BM that we have categorised within a new ABC system family (currently labelled NEW1; See Table 1). This system includes BP and IM proteins related to those of the MOS family and ABC proteins that are different to those from the MOS family. We previously identified a similar ABC system in the genomes of Burkholderia pseudomallei and Burkholderia mallei strains [45]. Clearly, experimental data is required to define the function of this system.

5. Differences between Brucella Species

Although there is similarity between the ABC system inventories of the Brucella strains studied in this work, we have identified systems that are absent in one or several Brucella species (Table 4). The systems that are absent from species are not critical for bacterial survival but could contribute to differences in the lifestyles or virulence of the Brucella species. Our data shows that there are ABC systems absent from all of the Brucella strains studied. In particular, BO (5 systems), BC (4 systems), and BA (4 systems) lack systems that are present in BM and/or BS. The absence of the ISB (formally ABCX) system from BO and BC is an interesting observation since the ISB systems are soluble complexes involved in labile [Fe-S] biogenesis, which is important in resistance to oxidative stresses. This could indicate that B. ovis and B. canis reside in environments that are low in oxygen or high in oxygen reducatants, or that they lack enzymes that need labile [Fe-S] centres [46, 47]. Furthermore, this difference may be a factor contributing to the reduced virulence for humans of B. ovis and B. canis when compared to B. melitensis, B. suis, and B. abortus. The CDI system absent from B.ovis is comprised of two proteins, FtsE (ABC protein) and FtsX (IM protein) [48], and has been studied in E. coli and other bacteria including Bacillus subtilis [49] and Mycobacterium tuberculosis [50]. This CDI system is involved in cell division. E. coli mutants of ftsE show a reduced growth capacity [51]. The MKL system absent from BC may play a role in toluene tolerance, since Tn5 insertions within the ttgA2 gene coding for the MKL ABC protein in Pseudomonas putida elicited a toluene-sensitive phenotype [52].


NumberFamilySubfamilySubstrate/ FunctionTypeB. melitensisB. abortusB. suisB. ovisB. canis

IMBMEI1851
5CCMPossibly heme exportIMBMEI1852
ABCBMEI1853
6CDIInvolved in cell divisionIMBMEI0073, ftsX
ABCBMEI0072, ftsE
7CLSO antigen export systemABCBMEI1416, rfbB
IMBMEI1415, rfbD
13DPLPRTProteases, lipase, S-layer protein exportOMPBMEI1029
14DPLCHVBeta-(1 2) glucan exportIM-ABCBMEI0984
16DPLHMTInvolved in mitochondrial export systemsIM-ABCBMEI1743
IM-ABCBMEI1742
22FAEFatty acid exportIM-ABCBMEII0976
CYTPBMEI1040
31ISB (ABCX)Iron/sulphur centre biogenesisCYTPBMEI1042
ABCBMEI1041
ABCBMEI0964
36MKLInvolved in toluene toleranceIMBMEI0965, ttg2B
SSBMEI0963, ttg2C
IMBMEII0087
IMBMEI0361
60o228UnknownMFPBMEI0359
ABCBMEI0360
IM BruAb10085
61o228UnknownMFP BCAN_A1712
ABC BruAb10084
62o228UnknownMFP BOV_1617
IM-ABC BCAN_A0087

Excludes ABC systems involved in import; : gene absent in the Brucella species; +: gene present in the Brucella species; : pseudogene present in the Brucella species; Number: refers to ABC system number in the full inventories/alignments of Brucella ABC systems

6. Conclusions

In this study the ABC systems of B. melitensis strain 16 M, B. suis strain 1330, B. abortus 9-941, B. canis strain RM6/66, and B. ovis strain 63/290 have been reannotated using the ABCISSE database in order to provide a new and improved set of annotated Brucella ABC systems for the strains studied. The information obtained and the uniform annotation and classification of ABC systems in these closely related species has enabled a more detailed analysis of the roles of ABC systems in Brucella species, contributing to an improved understanding of Brucella lifestyle and pathogenicity. Previous analysis of the Brucella genomes has shown that there is over 90% genome similarity between the Brucella species [13, 14]. Similarly, the ABC system inventory compiled in this work reflects the close similarities of the Brucella species. However, despite the high genetic homology of Brucella, this work highlighted differences in the predicted numbers and functions of the ABC systems encoded by each Brucella species. It is widely accepted that the three species that may cause the most human brucellosis are B. melitensis, B. suis, and B. abortus (and occasionally B. canis). This study has shown that these four species of Brucella have a larger set of ABC systems encoded within their genomes than B. ovis, which is not known to cause human disease. Although it is difficult to ascertain the exact effect of the loss of these ABC systems on B. ovis, it is possible to hypothesise that, along with other genetic differences observed [15], they contribute to its overall reduced virulence in humans. It should also be noted there that four further Brucella strains have been genome sequenced since this work was completed: B. melitensis 63/9, B. abortus 2308, B. abortus S19, and B. suis Thomsen. Compiling ABC systems inventories of these strains may identify further differences between strains that may have biological relevance. Among the newly sequenced strains are B. suis Thomsen, a strain which is not known to cause disease in humans, and B. abortus S19, a vaccine strain. ABC system inventories of these strains would be of particular interest since they are considered less pathogenic than the wild-type strains and yet the reasons for this lack of pathogenicity are currently unknown. Overall, the identified differences observed in the ABC system inventory of the Brucella strains studied should contribute to a greater understanding of differences in the lifestyles of the Brucella species.

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