Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species

1471-2148-7-71 1471-2148 Research article Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species Gupta S Radhey gupta@mcmaster.ca Lorenzini Emily lorenze@muss.cis.mcmaster.ca

Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, L8N3Z5, Canada

BMC Evolutionary Biology 1471-2148 2007 7 1 71 http://www.biomedcentral.com/1471-2148/7/71 17488508 10.1186/1471-2148-7-71 21 12 2006 08 5 2007 08 5 2007 2007 Gupta and Lorenzini; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Background

The Bacteroidetes and Chlorobi species constitute two main groups of the Bacteria that are closely related in phylogenetic trees. The Bacteroidetes species are widely distributed and include many important periodontal pathogens. In contrast, all Chlorobi are anoxygenic obligate photoautotrophs. Very few (or no) biochemical or molecular characteristics are known that are distinctive characteristics of these bacteria, or are commonly shared by them.

Results

Systematic blast searches were performed on each open reading frame in the genomes of Porphyromonas gingivalis W83, Bacteroides fragilis YCH46, B. thetaiotaomicron VPI-5482, Gramella forsetii KT0803, Chlorobium luteolum (formerly Pelodictyon luteolum) DSM 273 and Chlorobaculum tepidum (formerly Chlorobium tepidum) TLS to search for proteins that are uniquely present in either all or certain subgroups of Bacteroidetes and Chlorobi. These studies have identified > 600 proteins for which homologues are not found in other organisms. This includes 27 and 51 proteins that are specific for most of the sequenced Bacteroidetes and Chlorobi genomes, respectively; 52 and 38 proteins that are limited to species from the Bacteroidales and Flavobacteriales orders, respectively, and 5 proteins that are common to species from these two orders; 185 proteins that are specific for the Bacteroides genus. Additionally, 6 proteins that are uniquely shared by species from the Bacteroidetes and Chlorobi phyla (one of them also present in the Fibrobacteres) have also been identified. This work also describes two large conserved inserts in DNA polymerase III (DnaE) and alanyl-tRNA synthetase that are distinctive characteristics of the Chlorobi species and a 3 aa deletion in ClpB chaperone that is mainly found in various Bacteroidales, Flavobacteriales and Flexebacteraceae, but generally not found in the homologs from other organisms. Phylogenetic analyses of the Bacteroidetes and Chlorobi species is also reported based on concatenated sequences for 12 conserved proteins by different methods including the character compatibility (or clique) approach. The placement of Salinibacter ruber with other Bacteroidetes species was not resolved by other phylogenetic methods, but this affiliation was strongly supported by the character compatibility approach.

Conclusion

The molecular signatures described here provide novel tools for identifying and circumscribing species from the Bacteroidetes and Chlorobi phyla as well as some of their main groups in clear terms. These results also provide strong evidence that species from these two phyla (and also possibly Fibrobacteres) are specifically related to each other and they form a single superphylum. Functional studies on these proteins and indels should aid in the discovery of novel biochemical and physiological characteristics that are unique to these groups of bacteria.

Background

The Bacteroidetes and Chlorobi presently comprise two of the main phyla within the Bacteria 123. The bacteria from the Bacteroidetes phylum (previously known as the Cytophaga-Flavobacteria-Bacteroides (CFB) group) exhibit a potpourri of phenotypes including gliding behavior and their ability to digest and grow on a variety of complex substrates such as cellulose, chitin and agar 45678. They inhabit diverse habitats including the oral cavity of humans, the gastrointestinal tracts of mammals, saturated thalassic brines, soil and fresh water 910111213. The Bacteroides species such as B. thetaiotaomicron and B. fragilis are among the dominant microbes in the large intestine of human and other animals 1415. These bacteria in the human colon are also important opportunistic pathogens and they are involved in causing abscesses and soft tissue infections of the gastrointestinal tract, as well as diarrheal diseases 15161718. Other bacteroidetes species, such as Porphyromonas gingivalis and Prevotella intermedia, are major causative agents in the initiation and progression of periodontal disease in humans 121920.

In contrast to wide distribution of Bacteroidetes species in diverse habitats, bacteria from the phylum Chlorobi occupy a narrow environmental niche mainly consisting of anoxic aquatic settings in stratified lakes (chemocline regions), where sunlight is able to penetrate 21222324. Some of these bacteria also exist as epibionts in phototrophic consortiums with other bacteria, particularly β-proteobacteria 2125. The Chlorobi, which are also commonly known as Green Sulfur bacteria, are all anoxygenic obligate photoautotrophs, which obtain electrons for anaerobic photosynthesis from hydrogen sulfide 222326. Although the Bacteroidetes and Chlorobi are presently recognized as two distinct phyla 13, these two groups are closely related in phylogenetic trees based on 16S rRNA as well other gene sequences 27282930. Conserved indels (i.e. inserts or deletions) in a number of widely distributed proteins (viz. FtsK, UvrB and ATP synthase α subunit), that are uniquely present in species from these two groups, also strongly indicate that these two groups of species shared a common ancestor exclusive of all other bacteria 30.

The species from the Bacteroidetes and Chlorobi phyla are presently distinguished from other bacteria primarily on the basis of their branching in phylogenetic trees 2327. We have previously described a 4 aa conserved insert in DNA Gyrase B as well as a 45 aa conserved insert in SecA protein that were specific for the Bacteroidetes species 30. In Chlorobi as well as Chloroflexi species, their light harvesting pigments are located in unique membrane-attached sac-like structures referred to as 'chlorosomes' 22243132. A number of genes involved in the synthesis of chlorosomes components in Chlorobi have been identified by genomic and mutational analysis 26 and a few of them, viz. Fenna-Matthew-Olson (FMO) protein 33, are unique for this group 3234. However, the number of characteristics that are either unique to species from these two phyla, or are commonly shared by members of these phyla, are very limited. In the past few years, complete genomes of several Bacteroidetes and Chlorobi species have become available (see Table 1). Additionally, sequencing of genomes for many other Bacteroidetes/Chlorobi species is at different stages of completion (see Table 1), but considerable sequence information for these genomes is available in the NCBI database.

Table 1

General Characteristics of Bacteroidetes/Chlorobi Genomes

Strain Name

Taxonomic Order

Genome Size (Mb)**

GC Content (%)

Protein Number

Reference#

Bacteroidetes

Porphyromonas gingivalis W83^#

Bacteroidales

2.34

48.3

1909

[58]

Bacteroides fragilis NCTC 9343^#

5.24

4184

[16]

Bacteroides fragilis YCH46^#

5.31

33.5

4578

[35]

Bacteroides thetaiotaomicron VPI-5482^#

6.29

4778

[15]

Gramella forsetii KT0803^#

Flavobacteriales

3.8

36.6

3559

[59]

Flavobacteria bacterium BBFL7*

35.0

2592

Flavobacteriales bacterium HTCC2170*

37.0

3478

Flavobacterium johnsoniae UW101*

35.2

4985

DOE-JGI

Flavobacterium sp. MED217*

39.8

3735

Cellulophaga sp. MED134*

38.2

2944

Croceibacter atlanticus HTCC2559*

33.9

2719

Polaribacter irgensii 23-P*

31.0

2557

Psychroflexus torquis ATCC 700755*

32–33.0

6751

Robiginitalea biformata HTCC2501*

56.4

3228

Tenacibaculum sp. MED152*

30.6

2679

Cytophaga hutchinsonii ATCC 33406^#

Sphingobacteriales

4.43

38.8

3785

CP000383

Salinibacter ruber DSM 13855^#

3.59

66.5

2801

[36]

Chlorobi

Chlorobium chlorochromatii CaD3^#

Chlorobia

2.57

44.3

2002

CP000108

Chlorobium limicola DSM 245*

2.4

51.3

2435

DOE-JGI

Chlorobium phaeobacteroides BS1*

45.5

3791

DOE-JGI

Chlorobium phaeobacteroides DSM 266*

2.4

48.3

2789

DOE-JGI

Chlorobaculum tepidum formerly Chlorobium tepidum TLS^#

2.15

2252

[24]

Chlorobium luteolum formerly Pelodictyon luteolum DSM 273^#

2.36

57.3

2083

CP000096

Chlorobium clathratiforme formerly Pelodictyon phaeoclathratiforme BU-1*

48.1

2762

DOE-JGI

Prosthecochloris aestuarii DSM 271*

50.1

2313

DOE-JGI

Chlorobium phaeovibrioides formerly Prosthecochloris vibrioformis DSM 265*

53.0

1747

DOE-JGI

^#Indicates a completely sequenced genome. The references to the published genomes are provided. For others that are fully sequenced but not published, accession numbers for the genomes are given.

* Indicates that these genomes are at draft assembly stages. The information regarding genome sizes etc. in these cases have been obtained from the NCBI microbial sequence database.

The revised names for a number of Chlorobi species are as proposed in Ref. 45.

# The sequences marked 'a' are being sequenced by Gordon and Betty Moore Foundation Marine Biotechnology Intiative; DOE-JGE, indicates Department of Energy Joint Genome Institute. For some of the completed genomes, which are not published, their accession numbers are provided.

The availability of genomic sequences provide an opportunity to carry out in depth studies to identify novel molecular characteristics that are unique to these groups of bacteria and can be used for their diagnostics as well as biochemical and functional studies. Earlier comparative genomic studies on Bacteroidetes/Chlorobi species have been limited to only a few species and they have focused on specific aspects. The studies by Kuwahara 35 and Cerdeño-Tárraga et al. 16, who sequenced the genomes of B. fragilis strains, revealed that these genomes contained extensive DNA inversions in comparison to B. thetaiotaomicron. These inversion events are indicated to be important in terms of generating cell surface variability in these bacteria to avoid their recognition by the immune system. Large expansion of genes involved in the biosynthesis of cell surface polysaccharides and other antigens was also noted in these genomes 1635. A comparative analysis by Eisen et al. 24 of C. tepidum TLS genome identified many probable cases of lateral gene transfers (LGTs) between this species and Archaea; in all about 12% of C. tepidum's proteins were indicated to be most similar to those from the archaea. Similarly, the analysis of S. ruber genome by Mongodin et al. 36 has identified many cases of potential LGT between S. ruber and haloarchaea, particularly involving the rhodopsin genes.

In our recent work, we have used comparative genomics to systematically identify various proteins that are uniquely found in either all members, or particular subgroups, of a number of important groups of prokaryotes. These studies have identified large number of proteins that are specific for alpha proteobacteria 37, chlamydiae 38, Actinobacteria 39, epsilon proteobacteria 40 and Archaea 41. Such genes and proteins, because of their specificity for different phylogenetic or taxonomic groups, provide novel means for diagnostics and evolutionary studies 3839424344 and for the discovery of important biochemical and physiological characteristics that are unique to these groups of prokaryotes. However, thus far no comparative study has examined different genes/proteins that are uniquely present in species from the Bacteroidetes and Chlorobi phyla or are commonly shared by species from these two groups. In order to identify proteins that are uniquely found in the Bacteroidetes and/or Chlorobi groups of species, we have carried out systematic blast searches on all open reading frames in the genomes of P. gingivalis W83, B. fragilis YCH46, B. thetaiotaomicron VPI-5482, G. forsetii KT0803, C. luteolum DSM 273 and C. tepidum TLS against all available sequences in the NCBI non-redundant (nr) database. This has led to identification of large numbers of proteins that are distinctive characteristics of species from different taxonomic groups within the Bacteroidetes phylum (e.g. specific for the Bacteroides genus, specific for the Bacteroidales and Flavobacteriales orders, or specific for the entire Bacteroidetes phylum). Additionally, large numbers of proteins that are specific for the Chlorobi species as well as some proteins that are uniquely shared by the Bacteroidetes and Chlorobi phyla have also been identified. This work also describes three conserved indels in important housekeeping proteins (viz. alanyl-tRNA synthetase, DNA polymerase subunit III and ClpB) that are distinctive characteristics of either the Chlorobi or the Bacteroidales-Flavobacteriales-Flexebacteraceae groups. Phylogenetic analyses of the Bacteroidetes and Chlorobi were also carried out based on a concatenated sequence alignment for 12 highly conserved proteins and the results of these analyses support the inferences derived from the species distribution of various molecular signatures.

Results

Phylogenetic analyses of Bacteroidetes and Chlorobi species

Table 1 lists some characteristics of various Bacteroidetes and Chlorobi genomes that have been completely sequenced as well as for many others that are currently being sequenced. The taxonomy of the Chlorobi species has undergone significant revision in the past few years leading to name changes and new taxonomic groupings for a number of species 45. The newly proposed and former names for some of the species that will be discussed in the present work are as follows: Chlorobium tepidum changed to Chlorobaculum tepidum; Pelodictyon luteolum changed to Chlorobium luteolum; Prosthecochloris vibrioformis changed to Chlorobium phaeovibrioides; Pelodictyon phaeoclathratiforme changed to Chlorobium clathratiforme. Although many of these species in the databases are still referred to by their former names, we have used the revised nomenclature in our work to interpret the results of evolutionary and comparative genomic studies.

Prior to undertaking comparative analyses of Bacteroidetes and Chlorobi genomes, phylogenetic analyses on these species were carried out to get an overview of their evolutionary relationships, which can serve as a reference point for comparative genomic analyses. Phylogenetic analysis of Bacteroidetes and Chlorobi species has been carried out previously using 16S rRNA sequences and a few isolated protein sequences 2728293046474849. However, recent studies show that analyses based on larger dataset derived from multiple genes/proteins sequences provide a more reliable phylogenetic inference 50. Hence, phylogenetic analyses for these species was carried out based on concatenated sequences for 12 highly conserved proteins involved in a broad range of functions (see Methods section). The final sequence alignment for phylogenetic analysis contained a total of 6998 aligned positions.

Phylogenetic trees were constructed using the neighbour-joining (NJ), maximum-likelihood (ML) and maximum-parsimony (MP) methods 51. The results of these analyses for the NJ and ML methods are presented in Fig. 1. The trees were rooted using the sequences for Deinococcus-Thermus species. The tree in both cases consisted of two well-resolved clades (100% bootstrap scores by both treeing methods), one comprising of various Chlorobi species and the other containing various Cytophaga-Flavobacteria-Bacteroides (CFB) species. In these trees, S. ruber appeared as a deep branching outgroup of the Chlorobi clade, but in view of the low bootstrap score of the node indicating this relationship and the long branch that separated them, this relationship was not reliable. The topology of various species in the MP tree was very similar, except that in this tree S. ruber formed the outgroup of Chlorobi as well as various other CFB group of bacteria (results not shown). In addition to the uncertain position of S. ruber, different species belonging to the genus Flavobacterium did not form a coherent phylogenetic group (Fig. 1). For most other Bacteroidetes species, sequence information for multiple species from the same genera was not available.

Figure 1

Neighbour-joining tree based on concatenated sequences for 12 highly conserved proteins

Neighbour-joining tree based on concatenated sequences for 12 highly conserved proteins. The tree was rooted using sequences for Deinococcus-Thermus species and numbers on the nodes indicate bootstrap scores in the NJ and maximum-likelihood analyses (NJ/MP). The branching position of G. forsetii, which became available after this analysis was completed, is not shown. However, our analysis of a smaller dataset indicates that it exhibits closest affinity for the flavobacteria Psychrobacter torquis (results not shown).

Phylogenetic analysis on the concatenated dataset was also performed employing the character compatibility approach 52. In this approach, all sites in the sequence alignment where only two amino acid states are found, with each state present in at least two species, are examined for mutual compatibility to find the largest clique of mutually compatible characters 5253545556. By removing all homoplasic as well as fast-evolving characters from dataset, this approach provides a powerful means for obtaining correct topology in difficult to resolve cases 5657. Our concatenated dataset for the 12 proteins contained 832 positions where only two amino acids were found, with each amino acid present in a minimum of two species. The mutual compatibility of these binary state sites was determined as described in the Methods section.

The compatibility analysis identified two largest sets of compatible characters (referred to as cliques) each containing 410 characters. These cliques were identical in all respects except that the relative branching positions of Chlorobaculum tepidum and Chlorobium chlorochromatii, which differed by a single character, were interchanged. A composite of these cliques, in which the branching positions of these two species are not resolved, is shown in Fig. 2. A large number of characters (i.e. 200) in this clique distinguished the Chlorobi-Bacteroidetes species from the two Deinococcus-Thermus species, which were included to serve as outgroup. The clique is comprised of two main clades, one consisting of various species belonging to the Bacteroidetes group and the other of different Chlorobi species. The species from each of these clades were distinguished by a large numbers of characters. In the Bacteroidetes clade, S. ruber was found to be the deepest branching lineage and its specific association with other Bacteroidetes species was supported by 21 uniquely shared characters, which is a highly significant result 57. Additionally, the two main orders within the Bacteroidetes viz. Bacteriodales and Flavobacteriales, for which sequence information is available from multiple species, were clearly distinguished based upon multiple characters. However, these analyses detected no uniquely shared character between the C. hutchinsonii and S. ruber. Although, these two species are currently placed in the order Sphingobacteriales, phylogenetic trees do not support a specific grouping of them (see Fig. 1). Different Flavobacterium species again did not group together indicating that this genus does not constitute a phylogenetically coherent taxon. Within the Chlorobi clade, Prosthecochloris aesturaii was found to be the deepest branching lineage, but branching order of other Chlorobi species was not resolved.

Figure 2

Character compatibility tree (or the largest clique of mutually compatible characters) based on two states sites in the concatenated sequence alignment for the 12 proteins

Character compatibility tree (or the largest clique of mutually compatible characters) based on two states sites in the concatenated sequence alignment for the 12 proteins. The clique consisted of 410 mutually compatible characters. The numbers of characters that distinguished different clades are indicated on the nodes. Rooting was done using the sequences for Deinococcus-Thermus species.

Comparative Genomic Studies on Bacteroidetes and Chlorobi Species

To identify proteins that are uniquely present in species from the Bacteroidetes and Chlorobi phyla at various taxonomic levels (genus and above), systematic Blastp searches were performed on each protein or ORF in the genomes of the following species: Bacteroides (P. gingivalis W83 58, B. fragilis YCH46 35, B. thetaiotaomicron VPI-5482 15); Flavobacteria (G. forsetii str. KT0803 59); Chlorobi (C. luteolum DSM 273 and C. tepidum TLS 24). These analyses have identified a large number of proteins that are specific for different taxonomic groups. A brief description of these signature proteins and their evolutionary significances are discussed below.

Proteins (or ORFs) that are Specific for the Species within the Bacteroidetes Phylum

The blast searches on various ORFs from P. gingivalis, B. fragilis YCH46 and B. thetaiotaomicron genomes have identified 27 proteins that are present in most of the species from the Bacteroidetes phylum (Table 2). In addition to most fully sequenced Bacteroidetes genomes, the homologs of these proteins are also present in most Bacteroidetes species whose genomes have been partially sequenced. One of these proteins, PG0448, is present in all of the Bacteroidetes species, whose genomes have been either partially or fully sequenced. Two other proteins, PG1850 and PG2092, are present in all fully as well as partially sequenced genomes, except those from the Bacteroides genus. The absence of these proteins in only the species from this genus is very likely due to selective gene loss from this lineage and their genes also likely originated in a common ancestor of the Bacteroidetes phylum. Similarly, four proteins viz. PG0449, PG0779, PG1679 and PG2066, are present in virtually all other Bacteroidetes genomes, but they are missing in C. hutchinsonii. Their absence again is very likely due to selective gene loss from C. hutchinsonii. Eight additional proteins viz. PG0202, PG0362, PG0399, PG0482, PG0621, PG01281, PG1367 and PG1394, are present in all other fully as well as partially sequenced Bacteroidetes genomes, but they are only missing in S. ruber. The absence of these proteins in S. ruber can also be explained by selective gene loss. However, in view of the fact that S. ruber branches very deeply in comparison to all other Bacteroidetes species (Figs. 1 and 2), it is also possible that their genes evolved in a common ancestor of the other Bacteroidetes species after the divergence of S. ruber.

Table 2

Proteins that are Specific for the Phylum Bacteroidetes

Protein Name

Accession No.

Length

Possible/Predicted Function

Comments

PG0202

NP_904537

165

Uroporphyrinogen-III synthase HemD, putative; COG1587, HemD; pfam02602, HEM4

Missing in S. ruber⁺

PG0362

NP_904673

722

Hypothetical

Missing in S. ruber

PG0399

NP_904705

156

Putative lipoprotein

Missing in S. ruber

PG0448

NP_904748

434

Toluene × outer membrane/transport protein (OMPP1/FadL/TodX); pfam03349

All species present

PG0449

NP_904749

441

TPR domain protein; cd00189, TPR; COG3071, HemY; COG4783, Putative Zn-dependent protease

Not found in F. johnsoniae and C. hutchinsonii

PG0482

NP_904777

143

Hypothetical protein

Missing in S. ruber

PG0621

NP_904906

182

Hypothetical protein

Missing in S. ruber

PG0779

NP_905041

157

ExbD, Biopolymer transport protein; COG0848

Not found in F. bacterium HTC, F. johnsoniae and C. hutchinsonii

PG1281

NP_905462

387

Putative DNA mismatch repair protein; pfam01713, Smr; COG1193, Mismatch repair ATPase

Not found in C. atlanticus and S. ruber⁺

PG1367

NP_905532

200

Hypothetical protein

Missing in S. ruber

PG1394

NP_905555

165

Putative trans-membrane

Missing in S. ruber

PG1626

NP_905755

554

Putative hemin receptor

Missing in C. hutchinsonii; also present in C. phaeobacteriodes.

PG1679

NP_905797

464

Putative trans-membrane

Not found in P. ruminicola and C. hutchinsonii

PG1850

NP_905940

302

Hypothetical protein

Missing in Bacteroides species⁺

PG2066

NP_906128

351

Putative lipoprotein

Missing in P. ruminicola and C. hutchinsonii

PG2092

NP_906153

419

Hypothetical protein

Missing in Bacteroides species

BF0296

YP_097579

988

Outer membrane assembly protein

Missing in P. gingivalis and S. ruber⁺

BF0439

YP_097722

565

Putative outer membrane protein probably involved in nutrient binding

Missing in P. gingivalis, and Tenacibaculum

BF0534

YP_097817

192

Putative acetyl-transferase

Missing in P. gingivalis, C. atlanticus and S. ruber

BF0665

YP_097947

531

Putative exported protein

Missing in P. gingivalis, and C. hutchinsonii

BF0751

YP_098036

577

Putative exported protein

Missing in P. gingivalis, P. torquis, R. biformata and C. hutchinsonii

BF1057

YP_098341

506

Putative exported protein

Missing in P. gingivalis, and C. hutchinsonii

BF1254

YP_098538

507

Putative exported protein

Missing in P. gingivalis, and C. hutchinsonii

BF1327

YP_098610

514

Putative exported protein

Missing in P. gingivalis, and C. hutchinsonii

BF3185

YP_100464

490

Putative exported protein

Missing in P. gingivalis, and C. hutchinsonii

BF3612

YP_100889

542

Putative exported protein

Missing in P. gingivalis and C. hutchinsonii

BF4330

YP_101602

538

Putative exported protein

Missing in P. gingivalis,, R. biformata and C. hutchinsonii

For the proteins listed here, all significant blast hits are from various Bacteroidetes species, except as noted below. These proteins are present in all of the Bacteroidetes species listed in Table 1, except as noted in the comments.

⁺For the protein PG0202, a significant hit is also observed from C. phaeobacteroides; For BF0296 significant hits also observed from P. aestuarii and C. phaeobacteroides.

Of the proteins listed here, the following proteins are homologous to each other: BF0751, BF1057, BF1327, BF3185; BF1254, BF3612, BF4330.

We have also come identified a 3 aa deletion in a conserved region of ClpB protease that is present in all other Bacteroidetes species, except S. ruber (Additional file 1). Similar to the genes for the above 8 proteins, this deletion likely occurred in a common ancestor of the other Bacteroidetes species after the branching of S. ruber. Besides Bacteroidetes species, this indel is also present in the ClpB homologs from C. phaebacteroidetes (only Chlorobi species containing this protein) and the archaeum Methanospirillum hungatei, which is likely due to LGT. The remaining proteins in Table 2, of which 7 (BF0751, BF1057, BF1327, BF3185; BF1254, BF3612, BF4330) are homologous to each other, are missing in 1 or 2 sequenced species (e.g. P. gingivalis, B. fragilis, C. hutchinsonii or S. ruber) and their distribution pattern can also be explained by similar mechanisms as discussed above. Except for a few proteins that show limited similarity to conserved domains (CDs) found in other proteins 60, most of the proteins in Table 2 are of unknown function.

Additional File 1

A conserved indel (3 aa deletion) in ClpB protein that is mainly specific for the Bacteroidales, Flavobacteriales and Flexibacteraceae species. Partial sequence alignment of the ClpB protein containing this indel region is shown. The boxed region is missing in the Bacteroidales, Flavobacteriales and Flexibacteraceae species. Dashes in the alignment show identity with the amino acid on the top line. The ClpB homologs from C. phaebacteroidetes and Methanospirillum hungatei also lack the boxed region, which could be due to LGT. The beta and gamma proteobacteria contain a larger insert in this region, which has likely occurred independently.

Click here for file

These searches have also identified several proteins that at present appear unique for the species from the Bacteroidales and Flavobacteriales orders. These proteins are listed in Table 3. Of these, the first 4 proteins viz. PG0336, PG1302, PG1537, PG2030 are present in nearly all complete as well as partially sequenced species from the above two orders, but they are not found in S. ruber as well as C. hutchinsonii. The latter two species, which show much deeper branching than all other Bacteroidales species (Figs. 1 and 2), are currently placed in the order Sphingobacteriales. The genes for the proteins listed in Table 3 have thus likely originated in a common ancestor of the Bacteroidales and Flavobacteriales after the divergence of Sphingobacteria. Thirty-seven additional proteins in Table 3 are also uniquely present in either all or many of the sequenced Bacteroidales species and a small number of flavobacteria species including G. forsetii. A large number of these proteins are only missing in P. gingivalis, which is likely due to gene loss. Of the proteins listed in Table 3, seven are indicated to be conjugative transposon proteins: TraJ, TraN, TraK, TraF, TraE and TraB (PG1251 and PG1479, PG1475, PG1478, PG1482, PG1483 and BF0127, respectively). Four of them are present in two clusters very close to each other (PG1478-PG1479, PG1482-PG1483), supporting their involvement in related functions 6162. The genes for these proteins have also likely evolved in a common ancestor of the Bacteroidales and Flavobacteriales, followed by gene losses in various species.

Table 3

Proteins that are Specific for the Bacteroidales and Flavobacteriales Orders

Genome ID No. [Accession No.]

Possible/Predicted Function

Genome ID No. [Accession No.]

Possible/Predicted Function

PG0336 [NP_904650]

Hypothetical protein

PG1276 [NP_905457]

DNA-binding protein, histone-like family

PG1302 [NP_905476]

Hypothetical protein

PG1389 [NP_905551]

DNA-binding protein, histone-like family

PG1537 [NP_905677]

Hypothetical protein

PG1444 [NP_905595]

Hypothetical protein

PG1251 [NP_905435]

Conjugative transposon protein TraJ

PG1475 [NP_905621]

Conjugative transposon protein TraN

PG2030 [NP_906097]

Hypothetical protein

PG1478 [NP_905624]

Conjugative transposon protein TraK

PG1492 [NP_905638]

Hypothetical protein

PG1479 [NP_905625]

Conjugative transposon protein TraJ

PG0302 [NP_904618]

Hypothetical protein

PG1482 [NP_905628]

Conjugative transposon protein TraF

PG0330 [NP_904645]

DNA-binding protein, histone-like family; smart00411, BHL

PG1483 [NP_905629]

Conjugative transposon protein TraE

PG0555 [NP_904845]

DNA-binding protein, histone-like family

PG1488 [NP_905634]

Hypothetical protein

PG0829 [NP_905084]

Hypothetical protein

PG1494 [NP_905640]

Hypothetical protein

PG0870 [NP_905118]*

Hypothetical protein

PG2040 [NP_906106]

DNA-binding protein, histone-like family

PG0875 [NP_905123]

TnpA; DNA replication, recombination & repair, COG2452

PG2127 [NP_906183]

Hypothetical protein

PG1206 [NP_905397]^c

Mobilizable transposon, tnpC protein

BF1773 [YP_099054]*

Probable truncated integrase; cd01185, INT_Tn4399

Missing in Porphyromonas gingivalis W83

BF0127 [YP_097410]

TraB

BF1727 [YP_099008]

Putative outer membrane protein maybe involved in nutrient binding

BF0136 [YP_097419]

Tetracycline resistance element mobilization: RteC

BF1860 [YP_099142]

Hypothetical protein

BF0146 [YP_097429]

Hypothetical protein

BF1926 [YP_211559]

Hypothetical protein

BF0319 [YP_097602]*

Putative exported protein

BF2130 [YP_099411]

Hypothetical protein

BF0342 [YP_097625]

Putative exported protein

BF2214 [YP_099495]

Hypothetical protein

BF1067 [YP_098351]

Hypothetical protein

BF3164 [YP_100443]

Putative lipoprotein

BF1422 [YP_098707]

Hypothetical protein

BF4258 [YP_101533]

Hypothetical protein

BF1567 [YP_098851]

Hypothetical protein

The first five proteins in this table (viz. PG0336, PG1302, PG1537, PG1626, PG2030) are present in all Bacteroidales and Flavobacteriales species listed in Table 1; The other proteins are present in many of the Bacteroidales and Flavobacteriales species.

*Also present in C. phaeobacteroides.

The following proteins are homologous to each other: PG0330, PG0555, PG1276, PG1389, PG2040; PG0829, PG1444, PG1488; PG1251, PG1479; BF1422, BF1860; BF1926, BF4258.

Proteins that are specific for the order Bacteroidales or the genus Bacteroides

There are 4 genomes for the Bacteroidales species (P. gingivalis W83, B. thetaiotaomicron VPI-5482 and B. fragilis strains: NCTC 9343 and YCH46) that have been fully sequenced. Additionally, sequence information for a large number of genes/proteins from Prevotella intermedia 17 and Prevotella ruminicola 23, which belong to this order is available in the in NCBI database (see Table 1). Our blast searches on proteins from P. gingivalis genome have identified 52 proteins that are uniquely shared by either all or most of the sequenced Bacteriodales species and whose homologs are not found in any other species, except where noted (Table 4). Thirty-nine of these 52 proteins are uniquely found in all 4 fully sequenced Bacteroidales species. These species also form a strongly supported clade in phylogenetic trees (Figs. 1 and 2). Thus, it is likely that the genes for these proteins evolved in a common ancestor of this order. The remaining 13 proteins are lacking in at least one of the Bacteroides species (noted in Table 4), which is likely due to gene loss. In addition to the sequenced Bacteroidales species, high scoring homologs for many of the above proteins were also found in the two Prevotella species. These latter homologs were detected via genomic blasts against partially sequenced genomes from these species (see Methods).

Table 4

Proteins Unique to the Bacteroidales Order

Genome ID No. [Accession No.]

Possible/Predicted Function

Genome ID No. [Accession No.]

Possible/Predicted Function

PG0018 [NP_904375]^x

hypothetical protein

PG1133 [NP_905341]

conserved hypothetical protein

PG0082 [NP_904431]⁺

putative exported protein

PG1139 [NP_905347]

conserved hypothetical protein; cd02966, Tlp_A_like_family

PG0125 [NP_904468]

conserved hypothetical protein

PG1214 [NP_905405]

hypothetical protein

PG0179 [NP_904515]⁺

putative exported protein

PG1301 [NP_905475]⁺

conserved hypothetical protein

PG0188 [NP_904523]^x

lipoprotein, putative

PG1333 [NP_905502]^x

putative exported protein

PG0216 [NP_904548]⁺

conserved hypothetical exported protein

PG1352 [NP_905517]

putative conserved hypothetical protein

PG0217 [NP_904549]⁺

cons. hypothetical exported protein

PG1388 [NP_905550]⁺

conserved hypothetical protein

PG0218 [NP_904550]⁺

conserved hypothetical exported protein

PG1441 [NP_905593]^x

lysozyme-related protein; cd00737, endolysin_autolysin; COG3772, phage-related lysozyme

PG0246 [NP_904573]⁺

putative DNA-binding protein

PG1442 [NP_905594]

TraB

PG0312 [NP_904628]⁺

putative transmembrane protein

PG1458 [NP_905606]^x

hypothetical protein

PG0326 [NP_904641]

hypoth; COG3637, Opacity protein & related surface antigens

PG1473 [NP_905619]⁺

conjugative transposon protein TraQ

PG0366 [NP_904677]^+#

hypothetical protein

PG1621 [NP_905750]

conserved hypothetical exported protein

PG0434 [NP_904735]⁺

putative transmembrane protein

PG1757 [NP_905859]^x

hypothetical protein

PG0541 [NP_904834]⁺

conserved hypothetical protein

PG1881 [NP_905968]⁺

putative lipoprotein

PG0574 [NP_904862]

hypothetical protein

PG1889 [NP_905974]^x

hypothetical protein

PG0717 [NP_904988]⁺

lipoprotein, putative

PG1945 [NP_906027]⁺

conserved hypothetical protein

PG0781 [NP_905043]⁺

putative membrane protein

PG2006 [NP_906077]⁺

conserved hypothetical membrane protein

PG0816 [NP_905074]^x

hypothetical protein

PG2079 [NP_906141]

conserved hypothetical protein

PG0831 [NP_905085]

Cons. protein maybe related to TraB

PG2083 [NP_906145]⁺

conserved hypothetical protein

PG0843 [NP_905095]^x

conserved hypothetical protein

PG2116 [NP_906174]^x

transposase

PG0851 [NP_905101]

Toprim domain protein

PG2130 [NP_906186]

FimX

PG0910 [NP_905150]

FHA domain protein, cd00060

PG2131 [NP_906187]⁺

60 kDa protein; OmpA, COG2885.2

PG0937 [NP_905172]

putative exported protein

PG2133 [NP_906189]^x

lipoprotein, putative

PG0961 [NP_905192]⁺

conserved hypothetical protein

PG2149 [NP_906203]

putative conserved exported protein

PG1050 [NP_905267]^x

putative lipoprotein

PG2168 [NP_906219]⁺

FimX

PG1125 [NP_905334]⁺

conserved hypothetical protein

PG2224 [NP_906265]^x

hypothetical protein

All significant hits for these proteins are observed from the following Bacteroidales species, for which sequence information is available in the NCBI or TIGR microbial sequence database. P. gingivalis W83, B. fragilis NCTC 9343, B. fragilis YCH46 , B. thetaiotaomicron VPI-5482, Prevotella intermedia 17, P. ruminicola 23. Unless noted below, these proteins are present in all of the above-mentioned species. Of these proteins, the following are homologous to each other: PG0179, PG2133; PG0217, PG0218; PG0816, PG1458; PG0831, PG1442; PG2130, PG2168.

⁺Not found at present in either 1 or both Prevotella species.

^xMissing in one of the Bacteroides species as well as Prevotella species.

^#Also present was C. phaeobacteroides BS1.

The majority of the Bacteroidales-specific proteins are hypothetical and some of them are indicated as putative exported proteins (Table 4). Some interesting proteins in this list include the FimX proteins (PG2130, PG2168) that are involved in fimbriae production, which is necessary for adhesion to host surfaces 63. Also of interest is the conserved hypothetical protein, PG1139, which shows slight but significant similarity to the conserved domain in the TlpA-like family, responsible for cytochrome maturation. One of the proteins PG0366 also had a significant hit from C. phaeobacteroides, which could be due to LGT 64. There are seven proteins in Table 4 (PG0216-PG0218, PG1441-PG1442, PG2130-PG2131) that are present in clusters of two or three, suggesting that they could form functional units. Further, a number of proteins in this table (viz. PG0179, PG2133; PG0217, PG0218; PG0816, PG1458; PG0831, PG1442; PG2130, PG2168) are homologous to each other, indicating that they resulted from gene duplication events.

The Bacteroides genus contains three fully sequenced genomes corresponding to B. thetaiotaomicron VPI-5482 and B. fragilis strains NCTC 9343 and YCH46. The blast searches on B. fragilis YCH46 genome have identified 185 proteins that are mainly specific for these species (Additional file 2) and their homologs are not found in P. gingivalis. For 10 of these proteins, significant similarity was also observed for at least one of the two Prevotella species, suggesting that within the order Bacteriodales, species from the Bacteroides and Prevotella genera may be more closely related to each other in comparison to P. gingivalis. Most of these proteins are of unknown functions, however, some have been annotated as transmembrane or lipoproteins. Thirty-nine of these proteins are present in clusters of two to four in the genome indicating that they could be involved in related functions. A number of proteins in this table are homologous to each other indicating that they have likely resulted from gene duplication events.

Additional File 2

Proteins that are specific for the Bacteroides Genus. All significant hits for these proteins are from the following sequenced Bacteroides species unless otherwise indicated: B. thetaiotaomicron VPI-5482, B. fragilis NCTC 9343 and YCH46.

Click here for file

Proteins that are specific for the order Flavobacteriales

The complete genome of the first flavobacteria species viz.G. forsetii KT0803 became available very recently 59. However, sequence information for a large number of other Flavobacteriales species, whose genomes are being sequenced (see Table 1), is available in the NCBI database. Our blastp and PSI-blast searches on different ORFs in the G. forsetii genome have identified 38 proteins that are uniquely present in virtually all of the Flavobacteriales species (Table 5). Twenty-six of these proteins are present in all Flavobacteriales species listed in Table 1, whereas the remaining 12 are missing in only one of the species. An additional group of 146 proteins are also specific for the Flavobacteriales, but they are missing in some flavobacteria species or limited to only a small numbers of flavobacteria (Additional file 3). Because the genomes for most of the Flavobacteriales species are not complete at the present time, these proteins were not separated into different groups.

Table 5

Proteins that are Specific for Species from the Flavobacteriales Order

orf No. [Accession No.]

Possible/Predicted Function

Genome ID No. [Accession No.]

Possible/Predicted Function

orf89 [CAL65078]^b

membrane protein

orf1826 [CAL66812]

hypothetical protein

orf92 [CAL65081]

secreted protein

orf1872 [CAL66858]

hypothetical protein

orf107 [CAL65096]

membrane protein

orf2280 [CAL67264]^c

hypothetical protein

orf110 [CAL65099]

conserved hypothetical protein

orf2667 [CAL67651]

conserved hypothetical protein

orf191 [CAL65180]

membrane or secreted protein

orf2698 [CAL67682]

secreted protein

orf403 [CAL65392]^b

hypothetical protein

orf2700 [CAL67684]

hypothetical protein

orf509 [CAL65498]^c

hypothetical protein

orf2718 [CAL67702]

hypothetical protein

orf612 [CAL65599]^b

secreted protein

orf2731 [CAL67715]^b

secreted protein

orf983 [CAL65970]^a

hypothetical protein

orf2756 [CAL67740]

secreted protein

orf995 [CAL65982]

phospholipid/glycerol acyltransferase; smart00563, PlsC

orf2825 [CAL67809]

secreted protein

orf998 [CAL65985]

membrane protein

orf2844 [CAL67828]

membrane protein

orf1059 [CAL66046]

membrane protein

orf2917 [CAL67899]

secreted protein

orf1078 [CAL66065]^a

membrane or secreted protein

orf2939 [CAL67921]

hypothetical; COG1577, ERG12

orf1453 [CAL66440]

secreted protein

orf3043 [CAL68025]

hypothetical protein

orf1469 [CAL66456]^a

secreted protein

orf3076 [CAL68058]^e

hypothetical protein

orf1555 [CAL66542]

secreted protein

orf3240 [CAL68223]

membrane protein

orf1618 [CAL66605]^d

secreted protein

orf3266 [CAL68249]^a

conserved hypothetical protein

orf1766 [CAL66752]

hypothetical protein

orf3313 [CAL68296]

hypothetical protein

orf1776 [CAL66762]

hypothetical protein

orf3501 [CAL68484]

conserved hypothetical protein

Unless otherwise indicated, all significant hits for the proteins listed in this table are from the following Flavobacteriales species, for which sequence information is presently available. G. forestii KT0803, F. bacterium BBFL7, F. bacterium HTCC2170, F. johnsoniae UW101, Flavobacterium sp. MED217, Cellulophaga sp. MED134, C. atlanticus HTCC2559, P. irgensii 23-P, P. torquis ATCC 700755, R. biformata HTCC2501, Tenacibaculum sp. MED152. The proteins are present in all of these species except as noted below:

^aMissing in Polaribacter irgensii 23-P

^bMissing in Flavobacterium johnsoniae UW101

^cMissing in Flavobacteria bacterium BBFL7

^dMissing in Psychroflexus torquis ATCC 700755

^eMissing in Robiginitalea biformata HTCC2501

Additional file 3

Proteins specific for Flavobacteria that are missing in several species. All significant hits for these proteins are also from Flavobacteriales species. However, unlike the proteins listed in Table 5, these proteins are either present in only a small number of Flavobacteria or are missing from many species.

Click here for file

Proteins that are unique for the Chlorobi Phylum

The genomes of three Chlorobi species viz. C. luteolum DSM 273,C. tepidum TLS, and C. chlorochromatii CaD3, have been fully sequenced. Our blast analyses on the C. tepidum and C. luteolum genomes have identified 51 proteins that are uniquely shared by species from this phylum (Table 6). In addition to the 3 completely sequenced genomes, homologs of these proteins are also present in six others Chlorobi species (see Table 1), for which sequence information is available in the NCBI database. The genes for these proteins likely originated in a common ancestor of various Chlorobi species, which form a distinct, strongly supported, clade in phylogenetic trees (see Figures 1 and 2). The vast majority of these proteins are of hypothetical or unknown functions. However, 5 of them are indicated to be involved in functions related to photosynthesis. Of these, Plut_0264 and Plut_0265 are clustered in the genome and they correspond to chlorosome envelope proteins C and A, respectively. The protein Plut_1500, which is indicated as bacteriochlorophyll A protein, corresponds to the FMO protein that is involved in the attachment of chlorosomes to the cytoplasmic membrane 34. The other two photosynthesis-related proteins, Plut_0620 and Plut_1628, are annotated as photosystem P840 reaction centre protein PscD and the photosystem P840 reaction centre cytochrome c-551, respectively 2432. Three additional chlorobi-specific proteins, Plut_1714-Plut_1716, are clustered together in the genome indicating that they may form a functional unit 61. There are 65 additional proteins that are also specific for the Chlorobi species (Additional file 4). However, unlike the proteins in Table 6, these proteins are missing in a number of the Chlorobi species and their species distribution does not show any clear pattern and these could involve gene loss or LGTs 65. However, the first 8 proteins listed in this additional file (viz. Plut_0107, Plut_0759, Plut_0762, Plut_0981, Plut_0985, Plut_1092, Plut_1145, Plut_1858) are only found in C. luteolum and C. phaeovibrioides. These two species form a strongly supported clade in various phylogenetic trees (Figs. 1 and 2) and a specific relationship between them is further supported by the unique presence of these shared proteins. For one of the proteins in this table, Plut_1345, a significant hit is also observed from C. hutchinsonii, which could be due to LGT 6465.

Table 6

Proteins that are Specific for the Chlorobi Species

Genome ID No. [Accession No.]

Possible/Predicted Function

Genome ID No. [Accession No.]

Possible/Predicted Function

Plut_0059 [YP_373992]

Hypothetical protein

Plut_1225 [YP_375130]

Hypothetical protein

Plut_0074 [YP_374007]

orfCR

Plut_1238 [YP_375143]

Hypothetical protein

Plut_0111 [YP_374044]

Hypothetical protein

Plut_1332 [YP_375234]

TPR repeat

Plut_0145 [YP_374078]

Hypothetical protein

Plut_1409 [YP_375311]

Hypothetical protein

Plut_0160 [YP_374093]

Hypothetical protein

Plut_1465 [YP_375367]

Hypothetical protein

Plut_0264 [YP_374195]

chlorosome envelope protein C

Plut_1469 [YP_375371]

Hypothetical protein

Plut_0265 [YP_374196]

chlorosome envelope protein A; Bac_chlorC, pfam02043

Plut_1491 [YP_375393]

Hypothetical protein

Plut_0278 [YP_374209]

Hypothetical protein

Plut_1500 [YP_375402]

FMO, BchlA protein

Plut_0282 [YP_374213]

Hypothetical protein

Plut_1517 [YP_375417]

Hypothetical protein

Plut_0295 [YP_374226]

Hypothetical protein

Plut_1608 [YP_375505]

Srm

Plut_0325 [YP_374256]

Hypothetical protein

Plut_1625 [YP_375522]

Hypothetical protein

Plut_0409 [YP_374340]

Hypothetical protein

Plut_1628 [YP_375525]

Photosystem P840 reaction center cytochrome c-551

Plut_0422 [YP_374353]

Hypothetical protein

Plut_1682 [YP_375579]

Hypothetical protein

Plut_0489 [YP_374420]

Hypothetical protein

Plut_1714 [YP_375611]

Hypothetical protein

Plut_0499 [YP_374430]

Hypothetical protein

Plut_1715 [YP_375612]

Hypothetical protein

Plut_0540 [YP_374467]

Hypothetical protein

Plut_1716 [YP_375613]

Hypothetical protein

Plut_0572 [YP_374498]

Hypothetical protein

Plut_1725 [YP_375622]

Hypothetical protein

Plut_0620 [YP_374546]

Photosystem P840 reaction center protein PscD

Plut_1742 [YP_375639]

Hypothetical protein

Plut_0666 [YP_374587]

Hypothetical protein

Plut_1743 [YP_375640]

Hypothetical protein

Plut_0713 [YP_374634]

Hypothetical protein

Plut_1746 [YP_375643]

Hypothetical protein

Plut_0779 [YP_374695]

Hypothetical protein

Plut_1933 [YP_375818]

Hypothetical protein

Plut_0950 [YP_374855]

Hypothetical protein

Plut_2003 [YP_375888]

orfCR

Plut_1012 [YP_374917]

Hypothetical protein

Plut_2041 [YP_375926]

Hypothetical protein

Plut_1195 [YP_375100]

Hypothetical protein

Plut_2100 [YP_375985]

Hypothetical protein

Plut_1217 [YP_375122]

Hypothetical protein

Plut_2117 [YP_376002]

Hypothetical protein

Plut_1223 [YP_375128]

Hypothetical protein

All significant Blast hits for these proteins are observed only from the following Chlorobi species for which sequence information is presently available: C. luteolum DSM 273, C. tepidum TLS, C. chlorochromatii CaD3, C. limicola DSM 245, C. phaeobacteroides BS1, C. phaeobacteroides DSM 266, C. clathratiforme BU-1, P. aestuarii DSM 271 and C. phaeovibrioides DSM 265. Of these proteins, the following proteins are homologous to each other:Plut_0059, Plut_1491; Plut_0074, Plut_2003.

Additional file 4

Chlorobi-specific proteins that are missing in some species. All significant hits for these proteins are also from Chlorobi species. However, unlike the proteins listed in Table 6, these proteins are not present in all Chlorobi species.

Click here for file

In addition to the proteins that are uniquely found in various Chlorobi species, we have also identified two large conserved inserts in two widely distributed proteins that are distinctive characteristics of the Chlorobi phylum. The first of these signatures is a 28 aa insert in the DNA polymerase III alpha subunit encoded by the dnaE gene that is required for chromosomal replication in bacteria 66. The large insert in DnaE is present in all of the Chlorobi homologs but it is not found in any other species (Fig. 3). A smaller insert of 3–4 aa is probably also present in this regions in some Bacteroidales species, but based on their different sizes and sequence characteristics, these inserts are of independent origin. The other Chlorobi-specific signature consists of a 12–14 aa insert in alanyl-tRNA synthetase (Fig. 4), which plays an essential role in protein synthesis. This insert is again present in all Chlorobi homologs but not found in any other species indicating that it provides a reliable molecular marker for this group.

Figure 3

Partial sequence alignments of the DnaE protein showing a large insert of about 28 aa that is uniquely present in Chlorobi homologs

Partial sequence alignments of the DnaE protein showing a large insert of about 28 aa that is uniquely present in Chlorobi homologs. The dashes (-) denote identity with the amino acid on the top line. Except for the Chlorobi species, this insert is not found in any other organism. Sequence information for only representative species from other groups of bacteria is shown. Abbreviations in the species names are: Bac., Bacteroides; Cb., Chlorobaculum; Chl., Chlorobium; Chrom., Chromobacterium; Clo., Clostridium; Pro., Prosthecochloris; Sym., Symbiobacterium; Flavo., Flavobacterium; Strep., Streptococcus.

Figure 4

Partial sequence alignments of alanyl-tRNA synthetase showing a conserved insert of about 12–14 aa that is a distinctive characteristic of Chlorobi homologs and not found in other bacteria

Partial sequence alignments of alanyl-tRNA synthetase showing a conserved insert of about 12–14 aa that is a distinctive characteristic of Chlorobi homologs and not found in other bacteria. The dashes (-) denote identity with the amino acid on the top line. Additional abbreviations: Geo., Geobacter; Sta., Staphylococcus; Thermo., Thermoanaerobacter.

Proteins that are uniquely shared by the Bacteroidetes and Chlorobi species

The Bacteroidetes and Chlorobi species generally branch very close to each other in phylogenetic trees 27282930. However, there are very few characteristics known that are uniquely shared by species from these two phyla. Our analysis has identified 3 proteins (PG0081, PG0649 and PG2432 in Table 7) that are uniquely found in virtually all of the fully as well as partially sequenced Bacteroidetes and Chlorobi genomes. These results are significant because Bacteroidetes or Chlorobi species do not share any protein in common with different species from any other group of bacteria. Of these proteins, the protein PG0081 is also found in Fibrobacter succinogenes. A close and specific relationship of F. succinogenes to the Bacteroidetes and Chlorobi groups was strongly suggested by our earlier work based on conserved indels in different proteins 30. This inference is reinforced by the unique presence of this protein in these different groups. The absence of the protein PG0649, which is present in all other Bacteroidetes and Chlorobi species, in S. ruber, is probably due to gene loss. Three other proteins, PG1818, PG1977 and BF2465 although they appear unique to the Bacteriodales and Chlorobi, their homologs are not detected in most Flavobacteria including G. forsetii. It is likely that the genes for these proteins also evolved in a common ancestor of the Bacteroidetes and Chlorobi phyla followed by gene losses in particular Bacteroidetes lineages. All of these proteins are of unknown functions except PG1818, which is annotated as a putative transmembrane protein with significant similarity to the conserved domain of the ResB-like family.

Table 7

Proteins that are Uniquely Shared by the Bacteroidetes and Chlorobi Species

Protein I.D. No. [Accession No.]

PG0081 [NP_904430]

PG0649 [NP_904929]

BF2432 [YP_099715]

PG1818 [NP_905917]

PG1977 [NP_906051]

BF2465 [YP_099748]

Length (aa)

725 aa

194 aa

1478

238 aa

668 aa

93 aa

Possible Function

Hypoth.

Putative transmembrane

Hypoth.

Bacteroidetes

P. gingivalis

B. fragilis NCT

B. fragilisYCH

B. thetaiotaomi.

Prev. intermedia

Prev. ruminicola

G. forestii

F. bacterium BBF

F. bacterium HTC

F. johnsoniae

Flavobacterium

Cellulophaga

C. atlanticus

Polibacter irgensii

Psychro. torquis

Rob. biformata

Tenacibaculum

Cyto. hutchinsonii

Salinibacter ruber

Chlorobi

Cb. tepidum

C. chlorochrom.

C. luteolum

C. limicola

C. phaeobac BS1

C. phaeobac DSM

C. clathratiforme

Prosthec. aesturii

C. phaeovibrioides

All significant blast hits for these proteins are from the indicated (marked by *) Bacteroidetes and Chlorobi species. For the protein PG0081, a homolog is also present in Fibrobacter succinogenes subsp. succinogenes S85 (identified by blast search against the partial sequence). The blank space indicates that no hit showing significant similarity was detected at the present time.

Discussion

This work has identified a large number of proteins that are specific for Bacteroidetes and Chlorobi species at various taxonomic levels. Homologs exhibiting significant similarity to these proteins are not found in any other bacteria, except in a few isolated cases. Among the proteins that are specific for the Bacteroidetes, 27 proteins are specific for the entire phylum as their homologs are present in species from all three main orders within this phylum. Many other proteins are limited to various clades within the Bacteroidetes phylum. These include 41 proteins that are common to the Flavobacteriales and Bacteroidales orders; 53 and 38 proteins that are specific for the Bacteriodales and Flavobacteriales orders, respectively; and 185 proteins that are specific for the Bacteriodes genus. We have also identified 51 proteins that are specific for the Chlorobi species and 6 proteins that are uniquely shared by the Bacteroidetes and Chlorobi phyla. Two large conserved inserts in the DnaE and AlaRS proteins that are distinctive characteristics of the Chlorobi species were also discovered in this work. In addition, a deletion in ClpB protein that is mainly specific for the Bacteriodales, Flavobacteriales and Flexibacteraceae was also identified. In earlier work, a number of conserved inserts that are specific for either the Bacteroidetes phylum (viz. SecA and Gyrase B) or commonly shared by the Bacteroidetes and Chlorobi species were also described. Based upon their specificity for the Bacteroidetes and Chlorobi species, these molecular markers provide novel and more definitive means for identifying and circumscribing species from these groups.

The species distribution patterns of these signature proteins and conserved indels strongly suggest that they or the genes for them have evolved at various stages in the evolution of these bacteria (Fig. 5). However, subsequent to their evolution or introduction in these genes, these genomic characteristics are stably retained in various descendents of these lineages with minimal gene loss or LGTs, as has also been found in other related studies 3738394041446768. The evolutionary relationship among the Bacteroidetes species as deduced from these signature proteins is in complete agreement with their branching pattern in phylogenetic trees (Figs. 1 and 2). The unique presence of several signature proteins as well as conserved indels in a number of essential proteins (viz. FtsK, UvrB and ATP synthase alpha subunit) by different Bacteroidetes and Chlorobi species provides compelling evidence that species from these two groups shared a common ancestor exclusive of all other bacteria. In earlier studies, a close relationship of Fiborbacteres to the Bacteroidetes and Chlorobi was also observed 230. The species from all these three groups were found to contain large conserved indels in RNA polymerase β ' subunit and serine hydroxymethyl transferase, that were not found in any other bacteria 30. The species from these three groups also branched in the same position based on distribution profiles of signature sequences in a number of other proteins and in different phylogenetic trees 3069. The unique shared presence of the protein PG0081 by all sequenced Chlorobi and Bacteroidetes species as well as Fibrobacter succinogenes, provides further evidence that species from these three groups form a single superphylum and that they shared a common ancestor exclusive of all other bacteria 30.

Figure 5

A summary diagram showing the evolutionary stages where different signature proteins and conserved indels that are specific for the Bacteroidetes and Chlorobi species have likely evolved or originated. Some of the conserved inserts that are specific for these groups or indicate their branching position relative to other bacterial phyla have been described in earlier work [30,43,69].

This paper also reports phylogenetic analyses of Bacteroidetes and Chlorobi species based on a concatenated alignment of 12 highly conserved proteins. The branching order of various species in the trees obtained using different phylogenetic methods were in general very similar with the clades corresponding to the Chlorobi species and the Cytophaga-Flavobacteria-Bacteroides species, well resolved from each other with 100% bootstrap scores. The species corresponding to the two main groups within the Bacteroidetes phylum (viz. the Bacteriodales and Flavobacteriales orders) were also clearly resolved. However, in the trees constructed by traditional phylogenetic methods such as NJ, ML and MP, the phylogenetic placement of S. ruber was not resolved. In all of these trees, S. ruber appeared either as a very deep branch of the Chlorobi clade (i.e. in NJ and ML trees) or as outgroup of both the Chlorobi and the CFB clades (MP tree). In contrast to these trees, when the same dataset was analyzed by means of the character compatibility or clique approach, S. ruber formed the deepest branch of the Bacteroidetes species and its specific association with this group was supported by 21 uniquely shared characters, indicating strongly that this affiliation was reliable 57. These results provide evidence that the character compatibility approach, which removes all fast-evolving as well as homoplasic sites from a given dataset, provides a powerful means for obtaining correct topology in cases, such as that for S. ruber, whose phyletic affinity has proven difficult to establish by traditional phylogenetic methods 13525657.

The cellular functions of most of the Bacteroidetes or Chlorobi-specific proteins identified in the present work are not known. A few of the Chlorobi-specific proteins are involved in chlorosome- or photosynthesis-related functions, which is expected as Chlorobi is one of the few bacteria phyla that possesses photosynthetic ability 2231323470. A number of other proteins exhibit weak sequence similarity to conserved domains in certain other proteins, but considering that the overall sequence similarity is not significant, the actual functions of these proteins could be quite different. Therefore, an important task for the future is to determine the cellular functions of these Bacteroidetes or Chlorobi specific proteins. Likewise, it is also of much interest to determine the functional significance of the conserved indels in SecA, Gyrase B and ClpB proteins that are distinctive characteristics of the Bacteroidetes 30, and of the inserts in DnaE and AlaRS proteins that are specific for the Chlorobi species. The retention of these signature proteins and conserved indels by all species from these groups strongly suggests that they are functionally important for these bacteria. Hence, further studies on these molecular signatures should lead to the discovery of novel biochemical and physiological characteristics that are unique to these bacteria. The primary sequences of many of these genes/proteins that are specific for the Bacteroidetes or Chlorobi species are highly conserved and they provide novel means for identification of both known as well as novel species belonging to these groups by means of PCR-based and immunological methods. Several Bacteroidetes species play central role in the initiation and progression of periodontal diseases in humans 12181958. Hence, the proteins that are specific to these bacteria also provide important potential targets for development of therapeutics and vaccines for treatment and prevention of periodontal diseases.

Methods

Identification of Proteins that are Specific for Bacteroidetes and Chlorobi

The blastp searches were carried out on each ORF in the genomes of P. gingivalis W83 58, B. fragilis YCH46 35, B. thetaiotaomicron VPI-5482 15, G. forsetii KT080 59, Chlorobium (Pelodictyon)luteolum DSM 273 and C. tepidum TLS 24, to identify proteins that are specific for the Bacteroidetes and Chlorobi phyla at different taxonomic levels. The blastp searches were performed against all organisms (i.e. using the NCBI non-redundant (nr) database) with default settings except that the low complexity filter was not used 71. The proteins that were of interest were those where either all significant hits were from these groups of species or which involved a large increase in E values from the last Bacteroidetes-Chlorobi hit to the first hit from any other organism and the E values for the latter hits in most cases > 10^-4, which indicates a weak similarity that could occur by chance. However, higher E values were sometimes acceptable particularly for smaller proteins as the magnitude of the E value depends upon the length of the query sequence. All promising proteins were further analyzed using the position-specific iterated (PSI)-blast program 71. This program creates a position-specific scoring matrix from statistically significant alignments produced by the blastp program and then searches the database using this matrix. The PSI-blast is more sensitive in identifying weak but biologically relevant sequence similarity as compared to the blastp program 71. In the present work, a protein was considered to be specific for a given group if all hits producing significant alignments were from that group of species. However, we have also retained a few proteins where 1 or 2 isolated species from other groups of bacteria also had acceptable E values, as they provide possible cases of lateral gene transfer. For all of the Bacteroidetes or Chlorobi-specific proteins identified in the present work, their protein ID's, accession numbers and any information regarding cellular functions (such as COG number or the presence of any conserved domain) are presented here. Preliminary sequence information regarding the presence of a homolog of a query protein in the partially sequenced genomes of P. intermedia, P. ruminicola and F. succinogenes subsp. succinogenes S85 were obtained via genomic blasts against The Institute for Genomic Research database for unfinished microbial genomes 72. In describing various proteins in the text, "PG," "BF," "BT," "orf", "Plut" and "CT" indicate the identification numbers of the proteins in the genomes of P. gingivalis W83, B. fragilis YCH46, B. thetaiotaomicron VPI-5482,G. forsetii KT080, C. (Pelodictyon) luteolum DSM and C. tepidum TLS, respectively.

Phylogenetic Analysis

The amino acid sequences for the 12 conserved proteins viz. RNA polymerase β subunit, RNA polymerase β ' subunit (RpoC), alanyl-tRNA synthetase (AlaRS), arginyl-tRNA synthetase, phenylalanyl-tRNA synthetase, elongation factor-Tu, elongation factor G, RecA protein, DNA gyrase subunit A, DNA gyrase subunit B, Hsp60 or GroEL protein and DnaK or Hsp70 protein, for different species were downloaded from the NCBI database and aligned using the ClustalX (1.83) program using the default settings 73. The sequences for two deep-branching species, D. radiodurans and T. aquaticus 27, were included in this dataset for rooting purposes. The sequence alignments for all 12 proteins were concatenated into a single large alignment containing 8899 positions. Poorly aligned regions from this alignment were removed with the Gblocks 0.91b program 74, using the default settings, except that allowable gap position was selected to half. This resulted in a final sequence alignment of 6998 sites, which was used for phylogenetic analyses. A NJ tree based on this alignment (bootstrapped 1000 time) was constructed based on Kimura's model 75 using the TREECON programs 76. Maximum-likelihood and MP trees were computed using the WAG+F model plus a gamma distribution with four categories 77 using the TREE-PUZZLE 78 and Mega 3.1 program 79, respectively. All trees were bootstrapped 100 times 80, unless otherwise indicated.

The character compatibility analysis on the concatenated alignment was carried out as described recently 57. Using the program "DUALSITE" 57, all sites in the alignments where only two amino acid states were found, with each state present in at least two species, were selected. All columns with any gaps were omitted. The sites where one of the states is present in only a single species are not useful for compatibility analysis. All useful two state sites were converted into a binary file of "0, 1" characters using the DUALSITE program and this file was used for compatibility analysis 57. The compatibility analysis was carried out using the CLIQUE program from the PHYLIP (ver. 3.5c) program package 81 to identify the largest clique(s) of compatible characters. The cliques were drawn and the numbers of characters that distinguished different nodes were indicated. The sequence information for G. forsetii, which became available after these analyses were completed 59 is not included in these trees.

Identification of conserved indels

Multiple sequence alignments for large numbers of proteins have been created in our earlier work 828384. These alignments were visually inspected to search for any indels in a conserved region that was uniquely present in C. tepidum (the only Chlorobi species present in these groups). The specificity of any potential indel for these groups was evaluated by carrying out by blastp searches on a short segment of the sequence (between 80–120 aa) containing the indel and the flanking conserved regions against the nr database. The purpose of these blast searches was to obtain information from all available homologs to determine the specificities of the indels.

Abbreviations

CD, conserved domain; CFB, Cytophaga-Flavobacteria-Bacteroides; Indel, insert or deletion; ORF, open reading frame; ORFans, open reading frames of unknown functions; AlaRS, alanyl-tRNA synthetase; RGC, rare genetic change; RpoC, RNA polymerase β '-subunit.

Authors' contributions

The initial blastp searches on various genomes were carried out by RSG with the computer assistance provided by Venus Wong. EL analyzed the results of these blast searches to identify various group-specific proteins and confirmed their specificities by means of PSI-blast and genomic blasts. RSG carried out the phylogenetic analyses and identified the conserved indels described here. RSG was also responsible for conceiving and directing this study and for the final evaluation of results. RSG was responsible for the preparation of the final manuscript. All authors have read and approved the submitted manuscript.

Acknowledgements

We thank Venus Wong and Yan Li for providing computer support for blast analyses and Beile Gao for help with some phylogenetic analysis. We thank the investigators at US DOE Joint Genome Institute and Gordon and Betty Moore Foundation Marine Biotechnology Initiative for making the genome data for various Bacteroidetes and Chlorobi species available in public databases prior to publication, which were of central importance in these studies. Blast searches against preliminary sequence data for the P. intermedia, P. ruminicola and F. succinogenes were performed at The Institute for Genomic Research website 72. This work was supported by a research grant from the Canadian Institute of Health Research.

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