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  • Research article
  • Open Access

Genome organisation of the Acinetobacter lytic phage ZZ1 and comparison with other T4-like Acinetobacter phages

  • 1, 2Email author,
  • 1,
  • 1,
  • 3,
  • 1,
  • 1,
  • 1,
  • 1,
  • 1,
  • 1 and
  • 2Email author
BMC Genomics201415:793

https://doi.org/10.1186/1471-2164-15-793

  • Received: 6 February 2014
  • Accepted: 10 September 2014
  • Published:

Abstract

Background

Phage ZZ1, which efficiently infects pathogenic Acinetobacter baumannii strains, is the fifth completely sequenced T4-like Acinetobacter phage to date. To gain a better understanding of the genetic characteristics of ZZ1, bioinformatics and comparative genomic analyses of the T4 phages were performed.

Results

The 166,687-bp double-stranded DNA genome of ZZ1 has the lowest GC content (34.4%) of the sequenced T4-like Acinetobacter phages. A total of 256 protein-coding genes and 8 tRNA genes were predicted. Forty-three percent of the predicted ZZ1 proteins share up to 73% amino acid identity with T4 proteins, and the homologous genes generally retained the same order and transcriptional direction. Beyond the conserved structural and DNA replication modules, T4 and ZZ1 have diverged substantially by the acquisition and deletion of large blocks of unrelated genes, especially in the first halves of their genomes. In addition, ZZ1 and the four other T4-like Acinetobacter phage genomes (Acj9, Acj61, 133, and Ac42) share a well-organised and highly conserved core genome, particularly in the regions encoding DNA replication and virion structural proteins. Of the ZZ1 proteins, 70, 64, 61, and 56% share up to 86, 85, 81, and 83% amino acid identity with Acj9, Acj61, 133, and Ac42 proteins, respectively. ZZ1 has a different number and types of tRNAs than the other 4 Acinetobacter phages, although some of the ZZ1-encoded tRNAs share high sequence similarity with the tRNAs from these phages. Over half of ZZ1-encoded tRNAs (5 out of 8) are related to optimal codon usage for ZZ1 proteins. However, this correlation was not present in any of the other 4 Acinetobacter phages.

Conclusions

The comparative genomic analysis of these phages provided some new insights into the evolution and diversity of Acinetobacter phages, which might elucidate the evolutionary origin and host-specific adaptation of these phages.

Keywords

  • Phage genome annotation
  • Phage genome organisation
  • Comparative genomic analyses
  • T4-like phage

Background

ZZ1, a novel sequenced lytic phage that can efficiently infect Acinetobacter baumannii clinical strains, was identified from fishpond water in Zhengzhou, China [1]. As is typical for T4-like virion morphology, the ZZ1 viral particle contains an isometric head and a contractile tail, which are visible with transmission electron microscopy. The phage was reported to have different antibacterial activity against three A. baumannii clinical strains (AB09V, AB0901, and AB0902). Of the host bacteria, AB09V is the most sensitive, and ZZ1 causes large and distinguishable plaque formation on a lawn of AB09V and is highly infectious with a short latent period (9 min) and a large burst size (200 PFU/cell) [1].

To date, the genomes of 12 Acinetobacter phages have been completely sequenced and published in the NCBI genome database. Five belong to the Myoviridae phage group, including 133, Acj9, Acj61, and Ac42, and four belong to the Siphoviridae phage group, including Abp1 [NC_021316.1], Bphi-B1251 [NC_019541.1], AB1 [HM368260.1] and YMC/09/02/B1251_ABA_BP [JX403940.1]. Of the remaining 3 phages, AB3 [NC_021337.1] belongs to the Podoviridae phage group; AP205 [NC_002700.2], an ssRNA virus, belongs to the Levivirus group; and the phage IME-AB2 [JX976549.1] is unclassified. An initial NCBI nucleotide BLAST analysis (BLASTN) of the complete genome sequence indicated that ZZ1 shares limited similarity with other sequenced phages. The sequences from 4 Acinetobacter phages, Acj9 [GenBank: NC_014663.1], Acj61 [GenBank: NC_014661.1], Ac42 [GenBank: NC_014660.1], and 133 [GenBank: NC_015250.1], were the most similar to that of ZZ1 [1]. The four Acinetobacter phages were recently deposited in GenBank and were previously annotated as T4-like phages [2].

The T4 phage superfamily is one of the best-characterised groups of Escherichia coli phages [3, 4]. Most of the known T4-like phages specifically infect certain strains of E. coli or other enterobacteria, but several T4-like phages can propagate in bacteria that are more phylogenetically distant, such as Vibrio, Aeromonas, Cyanobacteria, and Acinetobacter [59]. Although many T4-like phages have been sequenced, only a limited number of these phage genomes have been analysed in as much detail as the T4-like Acinetobacter phages.

Previous cross-genome comparisons of T4 and other T4-like phages [813] revealed that this family of phages shares a common core genome from an ancestral sequence encoding the DNA replication modules, virion structural proteins, and some conserved predicted proteins. Furthermore, some of the proteins with unknown functions are conserved in T4-like phage genomes, and some of the minor differences between these phages may be related to their adaptations to different host ranges [7, 14]. A previous study found that each of the 4 T4-like Acinetobacter phages, Acj9, Acj61, Ac42, and 133, has a unique set of ORFs that occupy ~35% of the genome. In other words, each represents a different type of T4-related phage genome [2]. However, to the best of our knowledge, no detailed bioinformatics analysis and comparative genomic analyses of ZZ1 compared to T4 and the other Acinetobacter phages have been reported. Although detailed information about the relationship between the hosts of ZZ1 and the hosts of the other 4 Acinetobacter phages is not available from the NCBI database and the current literature, it has been confirmed that the hosts of the 5 phages belong to Acinetobacter (see Table 1). These phages may have evolved from a common ancestor and switched hosts during their evolution. The similarities and the differences between them can improve our understanding of their evolutionary strategy. More importantly, it would be useful to identify regions that are variable between the genomes of different T4-like phages that might underlie host-specific adaptations. Here, we describe the genome organisation of the phage ZZ1, which infects A. baumannii yet shares a common ancestor with the E. coli phage T4. The comparative genomic analyses of ZZ1, T4, and the other 4 T4-like Acinetobacter phages not only provides insights into viral diversity and evolution but also offers an exciting opportunity to understand the host-specific adaptation mechanism of these phages.
Table 1

General genome features of ZZ1, T4 and the other completely sequenced T4-like Acinetobacter phages

Phage name

Bacterial strain used in phage isolation

Accession

Size (bp)

No. of predicted CDSs

Gene density

% coding sequence

Avg gene product size (aa)

GC%

ZZ1

Acinetobacter baumannii

NC_018087.2

166687

256

1.5

93.9

203

34.41

133

Acinetobacter johnsonii

NC_015250.1

159801

257

1.6

95.5

197

39.67

Acj9

Acinetobacter johnsonii

NC_014663.1

169947

253

1.5

93.3

208

40.03

Acj61

Acinetobacter johnsonii

NC_014661.1

164093

241

1.5

92.5

209

39.01

Ac42

Acinetobacter sp.

NC_014660.1

167716

255

1.5

94.9

207

36.37

T4

Escherichia coli

NC_000866.4

168903

278

1.6

97.8

197

35.30

Results and discussion

Annotation of the ZZ1 genome

Sequence assembly yielded a closed, circular sequence with 114 bp inverted terminal repeats, indicating that ZZ1 phage particles contain linear, circularly permuted genomic DNA, similar to phage T4 particles [2]. The single copy genome is 166,687 bp. Bioinformatics methods identified 256 putative protein-coding sequences. The lengths of these CDSs range from 34 to 1,303 amino acid residues (aa) and average 203 aa. There are approximately 1.5 genes per kbp, and 93.6% of the ZZ1 genome is predicted to encode proteins (Table 1). ATG [96% (247/256)] was the predominant initiation codon. Only 4 CDSs began with GTG, and 5 began with TTG. The predominant termination codons were TAA [69% (177/256)] and TGA [27% (68/256)]. We noted that most of the significant BLASTP hits (201 CDSs, 78.5%) were proteins from phages (most of them belonging to the characterised T4-like phages), and the remaining hits were unknown proteins encoded by bacteria and other organisms. Of the 256 CDSs from ZZ1, 97 were assigned a functional annotation (see the colour code for the CDSs in Figure 1). Only 3 (1.2%) have no BLASTP matches in the non-redundant protein sequences database, indicating that genes encoding new viral proteins were revealed by the characterisation of this phage. However, further Batch CD-Search analyses suggested that 17 of the 97 genes with functional annotations lack protein domain information. Of the 256 CDSs, 156 were conserved hypothetical proteins, and only 23 of the proteins (9%) had protein domain information (see Figure 2). Further functional analysis revealed that the 97 CDSs assigned putative functions could be classified into 12 functional categories according to previous descriptions of phage T4 [3] (see Figure 1 and Additional file 1). Most of the named functional proteins are highly conserved among T4-like phages and are either structural (36 CDSs) or involved in DNA replication, recombination, repair, packaging, and processing (21 CDSs) (see Figure 2 and Additional file 1).
Figure 1
Figure 1

Annotated genome map of phage ZZ1. CDSs are labelled with the name of the closest homolog, and thus T4 nomenclature is primarily indicated (bold italics). The numbers below the CDS arrows are the CDS ids used in the text, tables, and GenBank. Following convention, the map starts at the bottom left with the rIIA gene and ends at the bottom right with the rIIB gene. The individual CDSs are depicted as arrows, with the orientation of the arrows indicating whether the genes are on the Watson or Crick strand. The colour of the arrow identifies the functional category into which the homologous T4 gene was classified [3]. The colour code for gene function is provided in the bottom of the figure.

Figure 2
Figure 2

Summary of the 256 ZZ1 genes annotated by BLASTP and Batch CD-Search analyses. (A) Pie chart showing the relative abundance of genes with and without named functions, including 95 KFP (known function proteins), 158 CHP (conserved hypothetical protein), 23 CHP-D (CHP with protein domain), and 3 HP (hypothetical protein) genes. (B) Relative abundance of ZZ1 proteins in 12 functional categories: A, Transcription; B, Translation; C, Nucleotide metabolism; D, DNA replication, recombination, repair, packaging, and processing; E, Virion proteins; F, Chaperonins/assembly catalysts; G, Lysis; H, Host or phage interactions; I, Host alteration/shutoff; J, Homing endonucleases and homologs; K, Predicted membrane spanning proteins in unknown function proteins; L, Unknown function.

Comparative genomics of T4 and ZZ1

The determination of phage relatedness is not based exclusively on sequence similarity but also takes genome organisation into consideration [15]. The phage ZZ1 has similar virion morphology [1], genome size and number of CDSs compared to the coliphage T4 (168903 bp, 278 CDSs) (Figure 3). To further investigate the genomic similarities of T4 and ZZ1, we constructed comparative genome maps of ZZ1 and T4. The putative gene rIIA from ZZ1 was positioned on the minus strand (leftward transcription) and at the start of the map, following the T4 convention. Homologous genes are projected onto the T4 map, and the projections are colour-coded based on protein sequence similarity (see Figure 3). BLASTP analysis indicated that the ZZ1 CDS140 shows significant similarity to the putative vs gene (<7e-23 E value, ≥ 80% coverage, and ≥ 50% maximum identity) from the other 4 T4-like Acinetobacter phages, Acj9, Acj61, 133, and Ac42 (see Figure 3). However, when we compared the ZZ1 CDS140 to the set of all T4 proteins by aligning two or more sequences from BLASTP using the default parameters, no counterpart was found in the results. Further BLASTP analysis revealed that, of the 4 Acinetobacter phages, only phage Acj61 vs showed a slight similarity to the T4 vs (0.1 E value, 99% coverage, and 32% max identity). Similar results were observed in the annotation of ZZ1 CDS156, which showed significant similarity to the putative 57A (<1e-4 E value, ≥70% coverage, and ≥37% max identity) from phages Ac42 and Acj61 although no counterpart was found in the BLASTP results when we compared ZZ1 CDS156 to the set of all T4 proteins. Thus, we annotated ZZ1 CDS140 and 156 as hypothetical proteins (see Figure 1), and of the 256 CDSs from ZZ1, only 95 (37.1%) could be assigned a functional annotation, and 158 (61.7%) were conserved hypothetical proteins (see Figure 2). Overall, such gradual evolution of the T4 genes between these closely and distantly related phages may eventually provide some interesting insights into the particular steps of genome divergence.
Figure 3
Figure 3

T4-ZZ1 comparison genomic mapping and ZZ1 orthologous genes from the other 4 Acinetobacter phages. The genomes and coding regions of T4 and ZZ1 are drawn in parallel approximately to scale. Alignment of different genes is from T4 (upper line) and from ZZ1 (lower line). Following convention, the map starts at the top left with the rIIA gene and ends at the bottom right with the rIIB gene. Horizontal arrows indicate transcription direction. The likely function of the genes is indicated by the colour of the arrows as described in Figure 1. Genes sharing protein sequence identity are linked according to the colour key provided at the middle left. ZZ1 genes are annotated randomly with their gene order in the GenBank database. The map was artificially split into upper halves and lower halves. ZZ1 genes that are orthologous to the 4 other Acinetobacter phages are indicated by coloured boxes under the corresponding ZZ1 genes. The amino acid sequence identity of ZZ1 genes to these orthologous genes was also indicated by colour as described in the key provided at the upper right. The % coverage of ZZ1 genes to these orthologous genes is indicated by the grey boxes under each coloured shade or box according to the grey scale key at the upper right. The genes indicated by the grey vertical arrows share significant similarity with proteins from the 4 other Acinetobacter phages, but share no significant similarity with T4 proteins.

Notably, 110 of the 256 ZZ1 CDSs (43%) shared up to 73% amino acid sequence identity with T4 proteins (E value < 10-6) (see Figure 3 and Additional file 1). Long blocks of synteny containing homologous genes are interspersed with stretches that lack homology. The lower halves of the genome, which are closely related, include three separate clusters of rightward-transcribed genes, specifically: (i) a cluster of base plate wedge/head/tail genes (genes 53 to 24), (ii) a smaller base plate hub gene cluster in its vicinity (genes 51 to 54), and (iii) further away, a tail fibre gene cluster consisting of a few large genes (genes 34 to t). Two clusters of leftward-oriented non-structural genes separate the 3 rightward-oriented clusters and mainly encode proteins involved in nucleotide metabolism. The degree of sequence identity varied substantially. The degree of sequence conservation did not follow structural/non-structural gene divisions.

The region that displays the most significant difference between ZZ1 and T4 is located in the upper halves of the genome that exclusively encode leftward-oriented, non-structural genes (with the exception of one rightward-oriented unknown gene, CDS147), including a large DNA replication module. Large regions of nonaligned genome segments were thought to have resulted from genetic gains, losses, or replacements, i.e., events similar to those that have shaped the evolution of all microbial genomes in nature. For example, ZZ1 rIIA.1.60, 60.1 and mobA are flanked by 14 unknown genes and 19 genes were deleted between ZZ1 vs.1 (CDS141) and segB (CDS142). Further alignment and comparison of T4 genes that are homologous to ZZ1 revealed that the order and transcriptional direction of T4 genes are broadly maintained in the ZZ1 genome, which helped provide the phylogenetic distance between ZZ1 and T4. There were three major differences: 1) the rnlB gene was at the junction of 24 in the lower genome half in T4 but was adjacent to the CDS012 in the upper genome half of ZZ1 (see Figure 3); 2) the topoisomerase gene (39 + 60) and the DNA polymerase gene (43) were split and intact, respectively, in T4 but intact and split, respectively, in phage ZZ1; and 3) a cluster of Alt genes including three putative Alt-like genes differs between T4 and ZZ1. As shown in Figure 3, the transcriptional direction of the three ZZ1 Alt-like genes was different from the T4 Alt, revealing an unusual genomic organisation for the Acinetobacter phage ZZ1. Moreover, the first Alt counterpart (CDS209) is 695 aa in length and shares 98% coverage and 28% amino acid identity with the T4 Alt (total 682 aa in length). The second Alt-like gene (CDS210) is 229 aa in length and shares 35% amino acid identity with the T4 Alt segment that extends from 1 to 217 amino acids, and the third Alt analogue (CDS211) is 463 aa in length and shares 33% amino acid identity with the T4 Alt segment that extends from 409 to 643 aa. Apparently, the last two ZZ1 Alt-like genes resulted from an even splitting event from the ancestral Alt gene (see Figure 3). The duplication of the Alt gene was also present in the genomes of the Acinetobacter phage Ac42 (see Figure 4), the coliphage JS98 (NC_010105.1), and the Enterobacteria phage Bp7 (NC_019500.1), but the splitting of the Alt gene was not observed in other T4-like phages.
Figure 4
Figure 4

Divergence of the core gene organisation between T4 and T4-like Acinetobacter phages. The map was artificially split into upper and lower halves. The bars indicate identified ORFs and are drawn to scale. Genes transcribed in the forward direction (or transcribed rightwards) are displayed above those genes transcribed in the reverse direction (or transcribed leftwards). The functional category of T4 genes is indicated by the color-coded bars described in Figure 1. The numbers and acronyms shown directly above the color-coded bars refer to the gene names. Core and Quasicore genes described by Petrov et al. [2] are shown in red and blue font, respectively. Homologous signature genes, shared by T4 and the 5 T4-related Acinetobacter phages, are connected with light blue shading. Conversely, homologous unknown genes, which shared significant similarity with all 5 T4-related Acinetobacter phages but no significant similarity with T4 proteins, are linked by dark and light purple shading. Genes linked by dark purple shading are specific to the 5 T4-related Acinetobacter phages in the GenBank database. In addition, 4 signature T4 genes, which are linked by green shading, could reflect a dominant feature in the evolution of all 5 T4-related Acinetobacter phages.

T4-like phages were often shaped by gene duplications. For example, in T4, genes 23 and 24 share 29% amino acid identity [3], and 16 proteins (mostly hypothetical) were identified as likely to have been duplicated in the KVP40 lineage [8]. To further examine duplications, we aligned genes from ZZ1 with other ZZ1 genes using BLASTP at the amino acid level and BLASTN at the DNA level. Those with better matches (based on E value) were considered candidates for lineage-specific duplications. Using this method, 14 proteins were identified as likely to have been duplicated in the ZZ1 lineage (data not shown). We further reasoned that if the homologous genes are the result of duplication of an ancestral gene, and if the different degrees of sequence diversification of these duplicated genes resulted from the accumulation of nucleotide point mutations resulting from differential selection pressure, then the genes with lineage-specific duplications should have significant nucleotide sequence identities. However, although the duplicated genes have significant amino acid identities, no significant nucleotide sequence identities were observed. Thus, the similarity of the genes is more likely to be the result of convergent evolution than the result of duplication of an ancestral gene. For example, ZZ1 23 and 24 share 25% amino acid identity but negligible nucleotide sequence identity (data not shown). The 24 protein plays an interesting role in T4 head maturation. The T4 prohead consists of an outer shell (23) and an inner scaffold (22). When 24 is added to the prohead, maturation cleavage occurs: 23 loses its N-terminal portion, whereas 22 is degraded completely [16]. In addition, in phage KVP40, the duplication of three genes encoding proteins associated with the phage tail or the tail fibre (gp12, gp19, and gp37) suggests added flexibility in the range of host adaptation and the infection process [8]. In our study, duplication was observed in three putatively duplicated gp34 (CDS244) homologues (gp37, gp12, and gp36 compared to CDS247, CDS171, and CDS246, respectively), which encode tail fibre-associated proteins and share 29-30% amino acid identity with ZZ1 gp34. Overall, splitting and/or duplication followed by sequence diversification and new gene insertion might be a mode of T4-like phage evolution.

Similarities and distinctions in the genome features of the E. coli phage T4 and the T4-like Acinetobacterphages

Alignment of the ZZ1 genome with the T4-like phages in the Tulane database showed that ZZ1 was closely related to 4 Acinetobacter phages. Based on the total search score, the closest was Acj9, followed by Acj61, Ac42, and 133. No other Acinetobacter phages were uncovered. In DNA sequence dot plots, we observed a frequently interrupted but straight diagonal line between ZZ1 and the 4 phages (data not shown). Overall, their genomes are colinear but are frequently interrupted by replacements with unrelated genome segments of comparable lengths, especially in the first halves of their genome. Further comparison of these genome sequences (including T4) at the DNA level using Mauve showed remarkable synteny in five large conserved regions (>10,000 bp) (see Figure 5). The most conserved syntenic region covered the morphogenesis module as well as the DNA replication and metabolism module, which are consistent with previous analyses [2, 14].
Figure 5
Figure 5

Multiple genome alignment and the genomes of ZZ1 and 5 T4-like phages. Six genomes were compared using Mauve software, and similarity profiles were generated. Boxes with identical colours represent local colinear blocks (LCB) indicating homologous DNA regions shared by two or more genomes without sequence rearrangements. The relative locations of orthologous genes, shown by open boxes, reveal a high degree of synteny. White regions within LCBs represent nonidentical sequences.

Protein-by-protein comparison of the 5 phages using BLASTP and CoreGenes revealed that ZZ1 shares 179 (69.9%) protein homologues with Acinetobacter phage Acj9, 164 (64.1%) with Acj61, 157 (61.3%) with 133, and 143 (55.9%) with Ac42, although ZZ1 shares only 110 protein homologues with coliphage T4. In contrast, 101 protein homologues are present in T4 and in all 5 Acinetobacter phages, whereas 119 homologous genes are present in all 5 of the Acinetobacter phages (46.3 to 49.3% of their protein-coding genes), which is further evidence that ZZ1 and the 4 other Acinetobacter phages belong to the same genus (see Figure 3).

The full portrait of the T4 phage superfamily that has emerged from the many reported genomic comparisons [2, 911] is that the T4 superfamily can be distilled down to core signature genes, which are known as the “Core Genome” of the T4-related phages or T4-like Viruses [2]. The Core Genome primarily includes homologues of essential T4 genes, such as the virion structure and DNA replication genes. In contrast, the hyper plastic regions (HPRs) contain mostly novel genes of unknown function and origin [7, 14]. The Core Genome of the T4-related phages has been considered to consist of two genetic components: one highly resistant component was termed the Core genes, which are essential for all known conditions; and the other component, which is somewhat permissive to attrition in evolution, was termed the Quasicore genes and can be substituted or circumvented in certain genetic backgrounds of phage and/or bacterial hosts [2]. The genetic background for the Core Genome can vary considerably between T4 relatives, and thus, the number of the core genes that constitute the Core Genome depends on the precise subset of phages considered, which constitutes an important criterion for distinguishing between close and distant relatives [14]. A closer look at the components and organization of the Core Genome in the 6 T4-like phages (see Figures 3 and 4) shows that all 5 Acinetobacter phages share a Core Genome with T4 interrupted by several HPRs, which are where most of their divergence occurs. This finding is consistent with the previous observations of T4-like phages [2, 7, 11, 13, 14, 17]. All of the Core genes described by Petrov et al. exist in all 5 T4-related Acinetobacter phages and are indicated by the red font directly above the coloured genes bars in Figure 4. The topology of the set of T4 phage Core genes is also shared by all 5 T4-related Acinetobacter phages. Moreover, we observed that almost all the Quasicore genes described by Petrov et al. ( by the blue font directly above coloured genes bars in Figure 4) were shared by all 5 T4-related Acinetobacter phages, except for uvsX (RecA-like recombination protein), uvsY (uvsX helper protein), nrdC (thioredoxin), nrdG (subunits of an anaerobic ribonucleotide reductase complex), tk (thymidine kinase), 49 (Endonuclease VII, required for recombination and DNA packaging), cd (dCMP deaminase), and denA (Endonuclease II). These genes are permissive to attrition in evolution of all 5 T4-related Acinetobacter phages (see Figure 4). In addition, nearly half of the other T4 signature genes (indicated by the black font directly above coloured genes bars in Figure 4) are shared by all 5 T4-related Acinetobacter phages, including the gene topology. Thus, all 5 T4-related Acinetobacter phages use similar mechanisms to control propagation in their hosts. These phages all shared a common ancestral genome but, during the course of evolution, they have modified it in numerous ways. These conserved T4 genes allowed the 5 T4-related Acinetobacter phages to conserve their highly successful virion design and mode of replication. Notably, several major distinctive genome features in all 5 T4-related Acinetobacter phages (indicated by the green shading in Figure 4) could reflect a dominant feature in the evolution of all 5 T4-related Acinetobacter phages.

The most significant difference between the 5 T4-related Acinetobacter phages and T4 is in a series of HPRs, which are interspersed between the conserved T4 core sequences and especially enriched in the upper genome halves of all 5 T4-related Acinetobacter phages. These regions vary greatly in gene number and content. The HPRs were primarily composed of genes of unknown origin, but they do contain some identifiable sequences from bacteria and unrelated phages. Thus, the HPRs have been predicted to be the result of an evolutionary history of isolation within distinct hosts and extensive lateral gene transfer (LGT), i.e., importing genes or exchanges with diverse biological entities in nature [7, 18]. Our observations showed that all of the genes lack T4 homologues in the 5 T4-related Acinetobacter phage genomes and cannot be assigned a putative function, most of which likely appear to be homologous genes from other phages, bacteria or other organisms. Notably, of the 119 ZZ1 genes that have significant homology with genes present in 4 of the Acinetobacter phages, 31 have unknown functions. Of these 31 genes, 18, which are indicated by the vertical grey arrows in Figure 3 (the counterparts of the 18 ZZ1 genes in the 4 other T4-related Acinetobacter phages are linked by dark or light purple shading in Figure 4), share no significant similarity to T4 proteins. Moreover, most of these homologous genes maintain a consistent order and content in the 5 T4-related Acinetobacter phages (see Figure 4). Further, BLASTP analyses suggested that 9 of the 18 ZZ1 genes (CDS042, CDS047, CDS049, CDS060, CDS125, CDS128, CDS138, CDS196, and CDS217), whose counterparts are linked with dark purple shading in Figure 4, lack significant matches to any of the phage sequences in GenBank except for the 4 other Acinetobacter phages (E value < 10-5) and a few other organisms (E value > 0.1). In particular, 7 (CDS042, CDS047, CDS049, CDS060, CDS138, CDS196, and CDS217) share high similarities (>50%) with the other 4 Acinetobacter phages.

The diversity among phage “Pangenome” (the union of all the different naturally occurring ORFs that exist in T4-related phages [2]) is a reflection of the adaptations of a phage ancestor to a variety of evolutionary challenges, including encountering new host environments. LGT most certainly has played a role in such adaptations, and these adaptations may have been facilitated in part by certain particularities of the T4 phage recombination and gene expression systems [7, 14]. However, to date, there are few clues about the agents that might mediate such a transfer. T4 recombines most efficiently early in the infection before the host genome is degraded, and this process could facilitate the acquisition of host genes by the phage [19]. As little as 50 bp of homology (perhaps less) is sufficient for T4 recombination system to recombine at reasonable frequencies [20]. Thus, “semilegitimate” recombination that relies on the small but generally conserved regulatory signals in the intergenic regions (promoters, translation initiation regions, transcription terminators, etc.) could perhaps have mediated the acquisition of such foreign genes [21]. Once the foreign genes are acquired, the T4 expression system could exploit their endogenous bacterial promoters because these sequences are very similar to the early promoter sequences of the T4-type phages [11, 22]. Overall, different phages sharing a common ancestor undergo a specific and similar adaptation process for different bacterial strains that belong to the same genera or species. The existence of these highly conserved unknown homologous genes specific to Acinetobacter phages in HPRs could reflect the complex interactions of Acinetobacter phages with conserved cell components that are specific to Acinetobacter bacterial hosts and are distantly related to E. coli or other bacterial hosts. Theoretically, the uniqueness of homologous genes or certain sequences in specific phage genomes or lineages might help distinguish between the different clusters or types of phage and help predict the bacterial host range when treating the corresponding bacterial genera clinical isolates. Additional research is required to elucidate the highly conserved genes that are specific to Acinetobacter phages.

GC skews in the ZZ1 genome

Phage ZZ1 DNA contains only 34.4% GC, which is slightly lower than the value (38.9% to 39.2%) observed in sequenced A. baumannii strains [2326]. To date, it is the lowest reported GC content for sequenced T4-like Acinetobacter phages (see Table 1). The GC content of ZZ1 is comparable with that of the Enterobacteria phage T4 (35.3%). The mol% GC of the T4 genome is also substantially lower than that of its host (approximately 50% GC) [3]. The difference is in disagreement with previous studies suggesting that the GC content of phage genomes such as the mycobacteriophages [27] and Staphylococcus aureus phages [28] have a GC content similar to their respective hosts.

Although ZZ1 has a lower GC content, 12 of the predicted phage ZZ1 genes contain more than 40% GC, including one major head gene (23 counterpart/CDS187), three tail fibre genes (12 counterpart/CDS171, 37 counterpart/CDS247, and 36 counterpart/CDS246), one nucleotide metabolism gene (cd counterpart/CDS221), and seven unknown genes. Notably, the GC content of the ZZ1 23 gene is 40.5%, which is significant lower than the local GC content of T4 23 (45%) and the T4-like phage JS98 23 (47.6%) [17]. Gene 23 has the highest proportion of codons that are translationally optimal for the host (65%) in keeping with its very high level of expression; approximately 1,000 copies of the protein are needed per synthesised phage particle [3]. Interestingly, the GC content of the ZZ1 host, A. baumannii strains, is approximately 39% and is lower than the GC content of the host strains for T4 and JS98, which is 50.8%. If the GC content of phages and their hosts become more similar during extended co-evolution, the difference between the GC content of ZZ1 gene 23 and the GC content of gene 23 in the phage T4 and JS98 presumably reflects the differences in host range, GC content, and life history of the respective hosts. Thus, the low GC content of ZZ1 23 suggests that phage ZZ1 might have acquired the ability to infect A. baumannii strains over a long period of time.

One region was found to be devoid of CDSs, extending from 72,968 to 76,602. In an effort to determine whether this region served as the replication origin, we used GC-skew analysis [29]. A putative origin of replication in the region of nt 81009 and a putative terminus of replication in the region of nt 1 were revealed (see Figure 6). The putative origin of replication is close to but not within the CDS-devoid region. However, tRNA detection showed that the tRNA genes from phage ZZ1 were encoded between CDS149 and 153, and 2 clusters of tRNAs (4 tRNAs in each) were located near the three adjacent genes, CDS150, 151, and 152. The two regions were in this CDS-devoid region (as shown in Figure 1). A previous study revealed that the phage ZZ1 had a very short latent period of 9 min [1]. The large number of tRNA genes and their strategic locations might enable the phage to translate its sequence more efficiently, reducing its latency time and increasing its reproduction rate and thus its infectivity.
Figure 6
Figure 6

Cumulative GC skew analysis of the genome sequence. The global minimum and maximum are displayed in the cumulative graph. The minimum and maximum of a GC-skew can be used to predict the origin of replication (nt 81009) and the terminus location (nt 1).

Codon usage and tRNAs

Eight tRNA genes were predicted in the ZZ1 genome (see Table 2). The T4 genome also has 8 tRNA genes, whereas Ac42 has slightly fewer (6), and others have substantially more including phage 133 (16), Acj9 (19), and Acj61 (14), as shown in Figure 7. The different numbers and types of tRNAs present in the 5 Acinetobacter phages are consistent with a previous study of tRNAs in T4-like phages [7, 13]. In addition, although ZZ1 has a low mol% GC content (34.4%), 4 (50%) out of the 8 tRNAs recognise codons with A in the third position (see Figure 7).
Table 2

tRNA genes from ZZ1 and homologous tRNAs from 4 other Acinetobacter phages and T4

Locus tag

tRNA type (anticodon)a

Location (bp)

Length (bp)

G + C content

Similar hit in 4 Acinetobacterphages and T4b

Phagename

tRNA type (Anticodon)

tRNA location

(Coverage/identities)

ZZ1t001

Trp (CCA)

73037-73108

72

55.60%

Acj9

Cys (GCA)

81632-81707

51%/80%

     

Acj9

Trp (CCA)

78801–78872

100%/89%

133

Trp (CCA)

66679–66754

100%/90%

Acj61

Cys (GCA)

80595-80670

68%/79%

ZZ1t002

Pro (TGG)

73349-73425

77

50.60%

Acj61

Pro (TGG)

79527-79603

93%/75%

     

133

Pro (TGG)

67417-67493

64%/76%

ZZ1t003

Ser (TGA)

73639-73733

95

61.10%

    

ZZ1t004

Thr (TGT)

73887-73962

76

53.90%

Acj9

Thr (TGT)

79955-80030

100%/80%

     

Acj9

Lys (TTT)

79870–79945

72%/75%

Ac42

Thr (TGT)

79430–79505

53%/83%

133

Ile (GAT)

67500–67575

72%/75%

T4

Pro (TGG)

72206-72280

77%/83%

ZZ1t005

Cys (GCA)

75677-75753

77

57.10%

Acj61

Cys (GCA)

80595-80670

79%/89%

     

133

Cys (GCA)

69475–69550

79%/85%

Acj9

Cys| (GCA)

81632-81707

72%/86%

ZZ1t006

Met (CAT)

75945-76021

77

54.50%

Acj9

Met (CAT)

81715-81790

100%/84%

     

133

Met (CAT)

69740–69815

100%/84%

133

Met (CAT)

66679-66754

55%/83%

ZZ1t007

Arg (TCT)

76027-76102

76

53.90%

133

Arg (TCT)

68572-68647

100%/88%

     

Acj9

Arg (TCT)

79288–79363

92%/81%

Acj61

Arg (TCT)

80679-80755

71%/:87%

ZZ1t008

Sup (CTA)

76196-76269

74

51.40%

Acj9

Pyl (CTA)

82721-82793

98%/75%

aTwo tRNA scan tools, tRNAscan-SE and ARAGORN, were used for prediction. All of the predicted tRNA genes are located on the minus strand of the ZZ1 genome.

btRNAs homologous to ZZ1 in other phages revealed by nucleotide comparison (using BLASTn with the following cut-offs: coverage, >50% and E value, ≤10-6) are also located on the minus strand of the phage genomes.

Figure 7
Figure 7

Codon usage and tRNA availability in Acinetobacter phages. The total number of codons is 52,152 for phage ZZ1 (256 genes), 52,870 for phage Acj9 (253 genes), 50,605 for phage Acj61 (241 genes), 52,929 for phage Ac42 (255 genes), and 51,005 for phage 133 (257 genes). Optimal codons that have relative phage-encoded tRNA are indicated with black boxes. Phage-encoded tRNAs related to the highly used codons are shaded grey, as is the corresponding codon.

The exact function of phage-encoded tRNAs in the phage-infected cell is still not clear. They might be involved in the adaptation of the host translation apparatus to the demands of the phage codon usage pattern. In other words, the tRNAs overcome the phage codon usage problem, and the presence of tRNAs in a phage genome has been suggested to compensate for differences in codon usage between the phage and the host, corresponding to codons that are expected to be poorly translated by the host machinery [30]. Previous studies indicated that T4-encoded tRNAs are related to codons that are highly used in T4 genes but rarely used in the host and that the phage tRNAs can enhance the low expression of T4 late-stage protein genes through optimal codon usage in translation [3, 31]. Similarly, analysis of the ZZ1-encoded tRNAs indicated that over half of them (5 out of 8) might be related to the optimal codon usage of ZZ1 proteins (Figure 7). However, the codon usage frequencies of the 4 other Acinetobacter phages suggested that phage-encoded tRNAs might be unrelated to decoding the relatively more frequent codons in all of the genes (Figure 7). Thus, the functional role of the tRNA genes for these phages remains unclear. Although the types and numbers of phage-encoded tRNAs differ between the 5 phages, some consistency was observed. For example, all 5 phages encode Met-tRNA and Trp-tRNA, which are related to optimal codon usage, but Arg-tRNA, which was not related to optimal codon usage, was also common to all 5 phages (see Figure 7). Of the 8 tRNA genes in ZZ1, 6 (75%) shared up to 89 and 90% nucleotide sequence similarity to tRNAs from phage Acj9 and phage 133, respectively; 4 (50%) shared up to 89% nucleotide sequence similarity to the tRNAs from phage Acj61; and only 1 tRNA showed 83% sequence similarity with the tRNA-Thr from phage Ac42 (see Table 2). In addition, the ZZ1-encoded tRNA-Thr gene shared 83% identity with the T4-encoded tRNA-Pro gene (see Table 2). The high degree of conservation of some of the tRNAs suggests an important functional role. The number and type of homologous tRNA appears to confirm the relationship between ZZ1 and the other phages, suggesting some elements of vertical evolution in these tRNAs.

Mobile elements

The homing endonuclease genes are not genuine phage DNA; rather, they belong to intron-associated selfish DNA elements [32, 33]. There are 7 seg, 5 mob, and 3 intron nuclease (I-TevI to -III) genes in the T4 genome [3], which have efficiently invaded the T4 genome and are also frequently found in the DNA transaction module opposite the tail fibre cluster (I-TevI and segG) and the DNA replication module (segA, mobB, mobC, and I-TevII) (Figure 3). Inconsistent distribution of these elements has been described for T2, T4 and T6 phages [34]. One notable difference between the T4 and ZZ1 genomes is that ZZ1 appears to lack counterparts in the corresponding regions, except for two mobile genes, a seg-like gene and a mob-like gene. The ZZ1 seg-like mobile endonuclease (CDS142), which is located in the DNA replication module, has 34 to 54% similarity to 6 seg genes in T4 (segA, segB, segF, segC, segD, and segE). However, the ZZ1 seg-like gene has higher similarity with the seg counterparts of the other 4 Acinetobacter phages: 73% amino acid identity with the seg counterpart from Acj9, and 56 to 58% identity with seg counterparts from Acj61, 133 and Ac42. The ZZ1 mob-like homing endonuclease (CDS175), which was found in the cluster of neck genes, lacks sequence similarity with the corresponding T4 genes. Nevertheless it has 52% sequence similarity with the mob counterparts from Acj9 and 33 to 39% sequence similarity with the mob counterparts from 133 and Ac42. The other 4 Acinetobacter phages also lack mobile elements in the corresponding locations. Although each of them has two to four seg genes, no mob-like genes were found in phage Acj61, only one mob-like gene was found in phage 133 and Ac42, and only two mob-like genes were found in Acj9 (see Figure 4). T4 has three self-splicing group I introns, one each in td, nrdB, and nrdD [3] (see Figure 4). A few group I-like introns have been found in other phages, such as T4, the S. aureus phage Twort [35], the Bacillus phages I-BasI and I-HmuI [36], the Lactobacillus phage LL-H, and the Lactococcus phage r1t [37]. However, none of the three T4 intron nuclease genes were found in phage ZZ1, Acj61, or Acj9, and only one I-TevI-like homing endonuclease from the GIY-YIG family was found in the 133 and Ac42 genome (see Figure 4). These mobile element genes do not commonly exist in the T4-like phages, and the differences in mobile elements between the 5 Acinetobacter phages and T4 phage genomes are consistent with the results for another T4-like phage [7, 13] Apparently, there are ill-defined barriers to intron promiscuity in bacteriophages [38, 39].

Conclusions

We determined and revised the complete genome sequence of the phage ZZ1 that infects pathogenic A. baumannii strains. A total of 256 potential proteins and 8 tRNAs were predicted. The BLASTP analysis reveals that only a small portion of its proteins (110 proteins, 43%) are clearly related to coliphage T4 proteins and share up to 73% protein sequence identity with the corresponding T4 proteins. Further analysis revealed that 179, 164, 157, and 143 proteins from ZZ1 share up to 86, 85, 81, and 83% amino acid identity, respectively, with Acinetobacter phage Acj9, Acj61, 133, and Ac42 proteins, respectively. Nine ZZ1 genes lack significant matches to any of the phage sequences in the GenBank database except for the 4 other Acinetobacter phages. In addition, the high degree of conservation of some tRNAs between ZZ1 and the other T4-like phages suggests that they may have an important functional role in addition to overcoming the phage codon usage problem. The number and identity of the homologous tRNAs supports the evolutionary relationship between ZZ1 and the other phages, suggesting some elements of vertical evolution in these tRNAs. Overall, although more than 200 T4-like phages have been examined [4, 13], only a very limited number of the T4-like Acinetobacter phage genomes have been explored or exploited. As additional genome sequencing of Acinetobacter phage species are completed, more Acinetobacter phages similar to T4 might be discovered. Host-specific adaptation mechanisms might be revealed by a more comprehensive understanding of the genomic diversity within the Acinetobacter bacteriophage population in the future.

Methods

Bacterial and phage strains

A. baumannii AB09V was isolated from the sputum of one hospitalised patient at the Henan Province People’s Hospital in Zhengzhou, China. After obtaining the approval of the Life Science Ethics Committee of Zhengzhou University and written informed consent, sputum samples were collected for the purposes of this study. The automated system BD Phoenix (Becton Dickinson Diagnostic Systems, Sparks, MD, USA) was used on clinical samples for the identification of bacteria and for antibiotic susceptibility tests. Moreover, as the host of phage ZZ1, AB09V has been further confirmed as A. baumannii using sequence information derived from the 16S rRNA gene in our previous work [1]. Phage ZZ1 was propagated in the A. baumannii strain AB09V as previously described [1].

Phage genome resequencing

The nucleic acid from the phage ZZ1 was extracted and purified from phage lysate using a MiniBEST Viral RNA/DNA Extraction Kit Ver. 4.0 (TAKARA BIO Inc., Tokyo, Japan) according to the manufacturer’s protocol. Phage DNA was then sent to Zhejiang California International NanoSystems Institute for sequencing. Phage DNA was fragmented with a Covaris S220. After end-repair and ligation of adaptors, libraries were amplified by polymerase chain reaction (PCR), purified with a QIAquick® PCR extraction kit (Qiagen, Venlo, The Netherlands), and sequenced on an Illumina Solexa Sequencing platform (Illumina, San Diego, USA) with a read length of 2 × 250. The whole genome sequences of ZZ1, with a total length of 166,682 bp, were obtained [1]. However, when we analysed in further detail the entire ZZ1 genome to understand the genetic characteristics of this phage, we found many split genes, which were considered to be due to errors from the sequence read assembly. Thus, in this study, we amended these errors by PCR + sequencing directly from phage genomic DNA. Ultimately, the length of revised single copy ZZ1 genome was 166,687 bp.

Bioinformatics analyses

Open reading frames (ORFs) were identified using two bioinformatics software programs, GenMarkS [40] and fgenesV0 (http://linux1.softberry.com/berry.phtml). The predicted translational regions were corroborated by manual inspection. These CDSs were considered valid if they possessed at least 30 amino acids (aa), showed a putative ribosome binding site (RBS) at a convenient distance, and began with an AUG, UUG, or GUG codon. The BLASTP program (version 2.2.15) [41] from NCBI was used to search for sequence similarity of the predicted CDSs against the NCBI nonredundant protein sequence database. Protein domain searches were conducted through BLAST and by using Batch CD-Search [42]. Cumulative GC skew was measured with GenSkew at http://genskew.csb.univie.ac.at/. ZZ1 phage codon usage was analysed with the CUSP and CAI programs of the EMBOSS package, version 6.2.0 [43]. tRNAs were identified using the tRNAscan-SE server [44] and confirmed using the ARAGORN program [45] as well as by nucleotide comparison using BLASTN (http://blast.ncbi.nlm.nih.gov/Blast.cgi). TMpred was used to identify membrane-spanning regions in CDSs (http://www.ch.embnet.org/software/TMPRED_form.html).

Comparative genomics

The phage genome sequences downloaded from NCBI and the Tulane T4-like genome (http://phage.bioc.tulane.edu) are listed in Table 1. Basic genome features of all of the phages, such as their host specificity, taxonomy, and genome molecular type, were also collected from the NCBI database and the literature. The dot matrix view from NCBI was used to examine whole-genome similarity using the default parameters. Further genomic comparisons at the nucleotide level were made with Mauve 2.2.0 [46] using a progressive alignment with default settings. Comparisons at the proteomic level were made using CoreGenes (http://binf.gmu.edu:8080/CoreGenes2.0/custdata.html) [47].

Availability of supporting data

The ZZ1 sequence data were deposited at GenBank under accession number NC_018087.3, which replaces the previous accession number. The CDS prefix indicates a predicted protein coding sequence, followed by numbers specifying the locus tag in the GenBank file (i.e., CDS001 is locus ZZ1p0001). The GenBank accession numbers of the other phage genomes analysed in this study are listed in Table 1.

Abbreviations

CDS: 

Coding sequence

HPR: 

Hyper plastic region

LGT: 

Lateral gene transfer

ORF: 

Open reading frame

RBS: 

Ribosome binding site.

Declarations

Acknowledgements

This study was financially supported by funding from a Key Project of the Science and Technology Development of Henan Province Science and Technology Bureau (No. 142102310440), the Education Department of Henan Province (No. 2011C310014), and a Project of the Science and Technology Development of Henan Province (No. 201303199).

Authors’ Affiliations

(1)
Department of Pathogen Biology and Immunology, Henan Medical College, Shuanghu Road #8, Zhengzhou, 451191, P. R. China
(2)
Department of Pathogen Biology, Basic Medical College of Zhengzhou University, Kexue Road #100, Zhengzhou, 450001, P. R. China
(3)
Clinical Laboratory, Henan Provincial People’s Hospital, Zhengzhou, 450003, P. R. China

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© Jin et al.; licensee BioMed Central Ltd. 2014

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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