Identifying the Genes Responsible for Iron-Limited Condition in Riemerella anatipestifer CH-1 through RNA-Seq-Based Analysis.
Riemerella anatipestifer (R. anatipestifer, RA) is a Gram-negative bacterium that belongs to the family Flavobacteriaceae in the rRNA superfamily V . R. anatipestifer infection causes disease in ducks, geese, chickens, turkeys, and other waterfowl and birds . The disease presents as an acute or chronic septicemia characterized by meningitis, fibrinous pericarditis, perihepatitis, and other symptoms . The disease causes increased mortality and decreased weight and is estimated to result in huge economic losses to the duck industry each year worldwide. At present, at least 21 serotypes of R. anatipestifer have been identified in the world [2, 4].
Iron is one of the most important elements for bacterial growth, as it is an essential cofactor in many important enzymes involved in energy metabolism and nucleotide synthesis . Iron is the second most abundant metal on earth, but it exists primarily in the insoluble ferric oxide form under aerobic conditions, which is not available for bacterial growth . Inside the host, most iron is bound to iron-binding proteins, such as ferritin, transferrin, and lactoferrin. Iron could also be included in the heme of hemoproteins (the terminology "heme" was used when talking about hemoproteins) . Bacteria employ various mechanisms to capture iron from the outside . One of these mechanisms is the secretion of a small molecular compound, a siderophore, which sequesters iron from the outside environment by high-affinity interactions . Then, iron-bound siderophores are taken up by the bacteria through specific siderophore receptors and transport systems . Alternatively, some pathogens have specific cell surface receptors that bind hemin (the terminology "hemin" was used when talking about iron and protoporphyrin ring source) or hemoprotein and transport hemin to the cell or secreted hemophores that capture hemin from host hemoproteins and then deliver hemin to bacterial surface receptors . Therefore, iron-limited conditions are able to prompt most bacteria to upregulate the expression of genes related to iron/hemin uptake, such as iron/hemin transporters and siderophore biosynthetic enzymes [11-13].
R. anatipestifer requires iron and hemin to survive . Genome analysis has shown that R. anatipestifer codes for a large number of TonB-dependent receptors, a TonB family protein, two sets of TonB complexes, and an FeoAB system . In a previous study, we demonstrated that TonB1 and TonB2 are involved in hemin uptake by R. anatipestifer ATCC11845 . Moreover some hemin binding proteins were detected in R. anatipestifer CH-1 . However, other genes involved in iron/hemin uptake by R. anatipestifer are largely unknown. In this study, we analyzed the global transcriptomic changes in R. anatipestifer CH-1 under iron-limited conditions. Here, we observed wide-ranging effects on the transcripts of iron-related genes of R. anatipestifer CH-1 and identified some new genes involved in iron/hemin uptake.
2. Materials and Methods
2.1. Bacterial Strains and Growth Conditions. For transcriptome analyses, R. anatipestifer CH-1 was grown in tryptone soy broth (TSB) medium (Sigma, China) as the iron-replete condition, while the iron-limited condition was TSB supplemented with 100 [micro]M iron chelator 2,2'-dipyridyl (Dip). The bacteria were cultured at 37[degrees]C with shaking at 180 rpm/min. Then, they were harvested at OD600 = 0.6 for iron-limited cultures and OD600 = 1.1 for iron-replete cultures (Figure 1).
2.2. RNA-Seq. Total RNA extraction was performed using the RNeasy Protect Bacteria Mini Kit (QIAGEN, Cat. number 74524) using the protocol described by Liu et al. . A total amount of 3 [micro]g RNA per sample was used for the RNA sample preparations. RNA quantification, library preparation, and sequencing were performed at Beijing Novogene as described elsewhere. Then the clean data were obtained by removing reads containing adapter, reads containing ployN, and low-quality reads from raw data . The high-quality reads obtained for each library were shown in Table 1. Then the R. anatipestifer CH-1 genome (CP003787.1) and gene model annotation files were downloaded from genome website (https://www.ncbi.nlm.nih.gov/nuccore/CP0037871) directly, using Bowtie2-2.2.3 to build index and align clean reads of the R. anatipestifer CH-1 genome .
2.3. Real-Time PCR Validation of RNA-Seq. The differential expression of selected genes was validated by quantitative reverse transcription polymerase chain reaction (qRT-PCR) using the SYBR green-based detection system on a CFX Connect[R] Real-Time PCR Detection System (BioRad Laboratories, Hercules, CA) using the KAPA SYBR[R] FAST qPCR kit (KAPABIOSYSTEMS, Boston, USA). cDNA was synthesized from each RNA sample (1 [micro]g) using the HiScript[TM] Q RT SuperMix for qPCR (+gDNA wiper) (R123-01; Vazyme, Nanjing, China). Real-time PCR assays were conducted with the primers for real-time PCR listed in Table S1 in Supplementary Material, available online at https://doi.org/10.1155/2017/8682057. Quantitative PCR was performed on samples deposited in triplicate using the standard curve mode protocol in which the calibration curve was generated using serial fivefold dilutions of 100 ng of total RNA. The RNA quantity was normalized using a probe specific for 16S rRNA.
2.4. RNA-Seq Analysis. To quantify the expression level of genes, HTSeq v0.6.1 was used to count the read numbers mapped to each gene . Then, the FPKM (expected number of Fragments Per Kilobase of transcript sequence per Million base pairs sequenced) of each gene was calculated based on the length of the gene and the read counts mapped to this gene. Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor . In this study, we used the DEGSeq R package (1.20.0) to execute the differential expression analysis of two conditions . Corrected P value of 0.005 and log2 (fold change) of 1 were set as the threshold for significantly differential expression. To analyze the gene structure of R. anatipestifer CH-1, Rockhopper was used to identify operons and transcription start sites. This program can be used for efficient and accurate analysis of bacterial RNA-Seq data and can aid in the elucidation of bacterial transcriptomes . Moreover we used the aligned paired-end reads to infer the operonic structure of R. anatipestifer CH-1 transcripts. If genes obtained >20 reads aligning on both genes in a sequencing sample, they would be selected as potential in an operonic structure. Sequential genes that are present in operonic structure were merged together to form potential operonic transcripts (Table S2).
3. Results and Discussion
3.1. Growth ofR. anatipestifer CH-1 in TSB and TSB with Dip. To evaluate the effect of iron restriction on the growth of R. anatipestifer CH-1, we grew R. anatipestifer CH-1 in TSB and TSB with 100 [micro]M Dip, which restricts most iron. Figure 1 showed that the growth of R. anatipestifer CH-1 was seriously hindered when iron was restricted, indicating that iron is an essential element for R. anatipestifer. Thus, this condition was suitable for performing RNA-Seq.
3.2. General Assessment of Iron Limitation Transcriptomic Datasets. Over 95% of all clean reads aligned to coding regions of the R. anatipestifer CH-1 genome (Table 1). Since only one sample in the different iron condition was used to perform RNA-Seq, qRT-PCR validation was performed on the transcriptome data using a subset of 20 differentially regulated genes (Table S1). The transcriptome data generally corresponded well with the qRT-PCR data, with a Pearson correlation coefficient of 0.806 (Figure 2), illustrating that our RNA-Seq data were of suitable quality for transcriptome analysis.
Upon comparing cultures grown in TSB and TSB with Dip, overall differences in gene expression were observed (Figure 3). To examine these differences further, DEGs (differentially expressed genes) were identified using the DEseq package . A total of 463 DEGs were identified, including 80 upregulated (Table 2) and 383 downregulated genes (Table S3). These genes represent 23% of the genome (2038 genes) . The large number of DEGs suggests that iron-limited environments have global effects on R. anatipestifer CH-1. Since samples of different OD were used to perform RNASeq, this study can not exclude the fact that cell density might influence gene expression.
3.3. Genome-Wide Identification of R. anatipestifer CH-1 Genes in Operonic Structures. In addition to identifying gene boundaries, we drew on paired-end sequencing information to identify the R. anatipestifer CH-1 global operonic structure. In total, 377 genes were determined to be in operonic structures using this analysis, thus constituting 230 operons (Table S2). These genes represent 18% of the genome (2038 genes) .
3.4. Gene Ontology (GO) Annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway Mapping of DEGs. The DEGs were assigned to 26 functional groups by enrichment analysis of Gene Ontology (GO) assignments . In the three main GO categories of biological process, cellular component, and molecular function, genes in the role categories of "localization, transport, and establishment of localization" in biological process, "membrane" in cellular component or "receptor activity and transporter activity" in molecular function were notably up- or downregulated (Figure 4).
The biological functions associated with the DEGs were further analyzed in terms of enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways , and a total of 20 pathways were predicted (Figure 5). Among these pathways, "microbial metabolism in diverse environments," "ribosome," and "thiamine metabolism" were the most highly represented categories (Figure 5).
3.5. Iron Limitation Increased the Transcription of Putative Iron Acquisition Systems. Genome sequence analysis indicated that R. anatipestifer CH-1 encodes [Fe.sup.2+] and [Fe.sup.3+] acquisition systems . Once in the periplasm, [Fe.sup.2+] is taken across the inner membrane via a divalent metal uptake system, such as the Feo system of E. coli  and the Yfe system of Yersinia pestis . In this study, the predicted genesfeoB (B739_0594) andfeoA (B739_0595), which encode an [Fe.sup.2+] transporter, were highly upregulated in the iron-limited condition, suggesting a role in the uptake of ferrous iron (Table 2). Sequence comparison revealed that all of the sequenced R. anatipestifer genomes have homologues of FeoA and FeoB of R. anatipestifer CH-1, with similarities of 100% for FeoA and between 88% and 100% for FeoB. In turn, these R. anatipestifer CH-1 genes have 33.45% and 32.89% identities to the FeoA and FeoB products of E. coli, respectively. In E. coli, this operon is regulated by Fur and is induced in acidic conditions . The functions of FeoA and FeoB and their regulation in R. anatipestifer are underinvestigated.
In aerobic conditions, many bacteria produce siderophores to solubilize [Fe.sup.3+]. Then, siderophore-bound [Fe.sup.3+] is taken up by TonB-dependent receptors . Genome analysis revealed that there are at least 33 predicted TonB-dependent receptors in R. anatipestifer CH-1, some of which are predicted transporters for ferric-siderophore complexes or heme. In this study, 5 TonB-dependent receptors were upregulated (B739_0094, B739_0103, B739_0173, B739_1068, and B739_1416) in the presence of iron depletion. The expression levels of seven other putative TonB-dependent transporters (B739_0115, B739_0876, B739_1045, B739_1343, B739_0216, B739_0329, and B739_0389) (Table S3) were downregulated in the presence of iron depletion. Upregulated TonB-dependent receptors would be predicted to be involved in iron or hemin uptake, while the functions of all downregulated TonB-dependent receptors are presently unknown. Similar results have been obtained in other bacteria, such as Pseudomonas fluorescens .
TonB-dependent receptors rely on the accessory proteins ExbB, ExbD, and TonB for energy transduction. One TonB family protein and two sets of ExbB-ExbD-TonB were found and identified in R. anatipestifer . In other bacteria, such as E. coli  and Pseudomonas fluorescens , the tonB gene is negatively regulated by iron. However, the transcription of tonB genes in R. anatipestifer CH-1 was not significantly changed in the iron-limited condition. To ensure the validity of the result, we also used qRT-PCR to measure tonB gene transcription in iron-limited conditions. The result was coincident with that of RNA-Seq. These results suggested that, in contrast to many bacteria, the tonB systems of R. anatipestifer CH-1 are not regulated by iron.
Once siderophore-bound [Fe.sup.3+] is transported into the cytoplasm, the iron must be released from the siderophore. The first mechanism is that siderophore-bound Fe(III) is reduced to siderophore-bound Fe(II) followed by its spontaneous release due to the low affinity of iron Fe(II) with the siderophore. Another mechanism is that siderophore-bound Fe(III) is hydrolyzed by specialized enzymes, leading to a dramatic loss of complex stability and facilitating the subsequent removal of the iron  in a reduction process. In this study, a gene coding for a siderophore-interacting protein (B739_0608) was upregulated significantly in the presence of iron depletion. This siderophore-interacting protein is involved in iron acquisition and virulence in R. anatipestifer strain CH-3 . Surprisingly, among the upregulated genes, we did not find any homologue gene related to siderophore synthesis.
3.6. A Putative Polysaccharide Utilization Locus ofR. anatipestifer CH-1 Was Upregulated in Iron-Limited Conditions. In Capnocytophaga canimorsus, a member of the Bacteroidetes, a polysaccharide utilization system uses serotransferrin as an iron source . Each polypeptide encoded by this locus is required for this iron uptake activity . This type of system was named the iron capture system (ICS), and it contains seven genes: icsA, icsC, icsD, icsE, icsF, icsG, and icsH . In this study, we identified a gene cluster (B739_0094, B739_0095, B739_0096, B739_0097, B739_0098, B739_0099, B739_0100, B739_0101, B739_0102, and B739_0103) (Table 2) involved in polysaccharide utilization, the expression of which was upregulated in the presence of iron depletion. Sequence comparison showed that the homologues of icsC, icsD, icsE, icsF, icsG, and icsH from Capnocytophaga canimorsus are B739_0103, B739_0102, B739_0101, B739_0100, B739_0099, and B739_0098, respectively, in the R. anatipestifer CH-1 genome. The homologue of icsA, B739_1068, was not cotranscribed with the others. Interestingly, some genes that were upregulated in the gene cluster, such as B739_0094, B739_0095, B739_0096, and B739_0097, were not predicted to contribute to the ICS system. Additionally, the R. anatipestifer CH-1 genome contains at least 6 polysaccharide utilization systems. In iron-limited conditions, three of the genes (locus B739_0094-B739_0103, locus B739_2091-B739_2093, and locus B739_0310-B739_0312) were upregulated (Table 2), while three other genes (locus B739_0115-B739_0118, locus B739_0875-B739_0876, and locus B739_1044-B739_1045) were downregulated (Table S3). Why some loci were upregulated and some loci were downregulated in the iron-limited condition is not currently understood.
3.7. Iron Limitation Increased Transcription of Putative Hemin Acquisition Systems. In the host, heme-containing proteins, such as hemoglobin, can be used as the main iron source by pathogenic bacteria . Hemin uptake systems are regulated by iron in other bacteria [34, 35]. Here, putative genes involved in hemin uptake were more highly expressed in iron-limited cultures of R. anatipestifer CH-1 than in iron-replete cultures. Within the upregulated genes, the most highly expressed gene cluster was FepA-hmuY (B739_1416, B739_1417), which encodes a putative outer membrane ferrienterochelin, a colicin receptor and an HmuY-like hemophore protein. In Porphyromonas gingivalis, HmuY is a heme-binding lipoprotein associated with the outer membrane or secreted to the outside environment [36, 37]. Gene (B739_1415) adjacent to the FepA-hmuY operon was also upregulated in iron-limited medium. The functions of B739_1415, B739_1416, and B739_1417 in hemin utilization are underinvestigated in our group.
3.8. Transcription of Respiratory Chain Genes. In aerobic metabolism, the respiratory chain typically uses proteins that require iron as a cofactor . When R. anatipestifer CH-1 was grown in iron-limited medium, the expression of genes coding for cytochrome biogenesis protein (B739_0948), periplasmic cytochrome c552 subunit (B739_0946), and cytochrome C (B739_0186) were downregulated (Table S3). It indicated that iron restriction hindered R. anatipestifer aerobic metabolism. Similarly, in other bacteria, such as Pseudomonas fluorescens Pf-5, the transcription levels of genes encoding cytochrome c-type biogenesis proteins (PFL_1684-88) and subunits of cbb3-type cytochrome c oxidases (PFL_1922-25, PFL_2834) are downregulated in iron-limited versus iron-replete medium .
3.9. Transcription of Genes Related to Natural Competence. Natural transformation refers to the process by which bacteria can actively take up and integrate exogenous DNA. Natural transformation is a major mechanism of horizontal gene transfer (HGT) and plays a prominent role in bacterial evolution . The process of Vibrio cholerae natural transformation involves four steps: DNA-binding via type IV pili, DNA pulling via ComEA, DNA translocation via ComEC, and DNA recombination by the single-strand DNA-binding proteins DprA and RecA . Previously, we found that R. anatipestifer CH-1 is naturally competent . In R. anatipestifer CH-1, no putative type IV pilus locus is evident in the genome. In R. anatipestifer CH-1, two proteins that are predicted to be involved in the DNA uptake process, a ComEC homologue (B739_1095) and a gene encoding a single-strand DNA-binding protein (B739_1757), were downregulated in iron-limited conditions. One possibility for this phenomenon is that these proteins require iron for activity, as well as iron being predicted to be involved in the natural transformation process. This relationship between natural transformation and iron availability has not yet been described.
In this study, we examined the transcriptomic impact of iron limitation on R. anatipestifer CH-1 by comparing iron-limited TSB cultures with iron-replete TSB cultures. This transcriptome analysis identified numerous genes involved in R. anatipestifer CH-1 iron utilization. Under iron limitation, we observed changes in the transcription levels of genes related to iron homeostasis functions, such as the Feo system, the ICS system, and other iron uptake systems. Iron limitation also resulted in several unexpected responses, particularly the increased transcription of the ribosomal protein genes L18, L15, and L31. The data in this study were useful for identifying genes involved in iron utilization in R. anatipestifer CH-1 and for shedding light on the adaptation mechanisms of R. anatipestifer CH-1 in iron-limited environments, such as hosts.
Abbreviations RNA-Seq: RNA sequencing qRT-PCR: Quantitative reverse transcription polymerase chain reaction HGT: Horizontal gene transfer DEGs: Differentially expressed genes KEGG: Kyoto encyclopedia of genes and genomes GO: Gene Ontology ICS: Iron capture system FPKM: Expected number of Fragments Per Kilobase of transcript sequence per Million base pairs sequenced.
Conflicts of Interest
The authors declare that they have no competing interests.
MaFeng Liu and AnChun Cheng conceived and designed the experiments. MaFeng Liu and Mi Huang performed the experiments. Francis Biville, MingShu Wang, DeKang Zhu, RenYong Jia, Shun Chen, and KunFeng Sun analyzed the data. Ying Wu and Qiao Yang contributed reagents/materials/analysis tools. MaFeng Liu and Mi Huang wrote the paper. All authors have reviewed the manuscript. MaFeng Liu and Mi Huang contributed equally to this work.
This work was supported by the International S&T Cooperation Program of Sichuan Province (Grant no. 2016HH0052), the National Natural Science Foundation of China (Grant no. 31302131, http://www.nsfc.gov.cn/), the Research Fund for the Doctoral Program of Higher Education of China (Grant no. 20135103120006, http://www.cutech.edu.cn/cn/index.htm), the National Science and Technology Support Program (no. 2015BAD12B05), the China Agricultural Research System (CARS-43-8), and the Integration and Demonstration of Key Technologies for Duck Industrialization in Sichuan Province (2014NZ0030).
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MaFeng Liu, (1, 2, 3) Mi Huang, (1, 2, 3) DeKang Zhu, (2, 3) MingShu Wang, (1, 2, 3) RenYong Jia, (1, 2, 3) Shun Chen, (1, 2, 3) KunFeng Sun, (1, 2, 3) Qiao Yang, (1, 2, 3) Ying Wu, (1, 2, 3) Francis Biville, (4) and AnChun Cheng (1, 2, 3)
(1) Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
(2) Research Center of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan 611130, China
(3) Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan 611130, China
(4) Unite des Infections Bacteriennes Invasives, Departement Infection et Epidemiologie, Institut Pasteur, Paris, France
Correspondence should be addressed to MaFeng Liu; firstname.lastname@example.org and AnChun Cheng; email@example.com
Received 28 December 2016; Accepted 29 March 2017; Published 30 April 2017
Academic Editor: Ernesto Picardi
Caption: Figure 1: Growth curves of R. anatipestifer CH-1 in iron-limited and iron-replete media. Optical densities at a wavelength of 600 nm were taken from the 2nd to the 18th hours at intervals of 2 hours. Measurements were performed on triplicate samples.
Caption: Figure 2: Validation of RNA-Seq data. Correlation analysis of [log.sub.2]-based fold changes between RNA-Seq data and qRT-PCR data for 20 genes of R. anatipestifer CH-1. The chart depicts a plot of RNA-Seq [log.sub.2]-based fold changes versus qRT-PCR [log.sub.2]- based fold changes for transcripts of genes in cultures of R. anatipestifer CH-1 grown in TSB+Dip medium versus TSB medium. A Pearson correlation coefficient of 0.806 was noted.
Caption: Figure 3: Differential gene transcription in cells grown in iron- limited TSB medium compared to TSB medium. The x-axis of the chart shows log2-based fold changes of transcripts in cells grown in iron-limited medium or TSB medium. The y-axis of the chart shows the statistical significance. Each dot in the chart represents one annotated gene. Red dots: upregulated, green dots: downregulated, and blue dots: no significant change.
Caption: Figure 4: Role categories of genes from the transcriptome data. The numbers of genes that are up- and downregulated in R. anatipestifer CH-1 grown in iron-limited TSB medium versus TSB medium are categorized according to role categories. Some genes are listed in more than one category and so may be counted more than once.
Caption: Figure 5: KEGG pathway enrichment analysis of differentially expressed genes between TSB and TSB with Dip. The y-axis of the chart shows the pathway name. The x-axis of the chart shows the Richness factor. The size of each point shows the number of genes in the pathway. The color of each point shows the Q value range.
Table 1: Summary of Illumina RNA-Seq data. Sample Total reads Total mapped Clean data * (Gb) CH_1TSB 17948156 17106745 2.24 CH_1TSBD 21489778 21099289 2.68 Sample Percentage of sequence reads mapped CH_1TSB 95.31% CH_1TSBD 98.18% * Clean data were obtained from raw data by removing reads containing adapter and poly-N and low-quality reads. Table 2: Genes upregulated in Riemerella anatipestifer CH-1 in iron-depleted conditions. Gene ID Gene name log2.Fold_ P value change. 13715178 B739_0074 1.289 0.00021641 13715197 B739_0093 2.8509 2.72E - 108 13715198 B739_0094 1.2615 8.08E - 28 13715199 B739_0095 1.5902 5.31E - 23 13715200 B739_0096 3.3265 4.50E - 246 13715201 B739_0097 3.1172 1.67E - 115 13715202 B739_0098 3.3417 0 13715203 B739_0099 3.5712 5.25E - 128 13715204 B739_0100 3.5135 5.06E - 149 13715205 B739_0101 3.0646 1.23E - 132 13715206 B739_0102 3.4075 0 13715207 B739_0103 3.8099 0 13715231 B739_0127 1.275 1.56E - 06 13715277 B739_0173 3.3109 2.55E - 195 13715278 B739_0174 3.6434 5.92E - 216 13715279 B739_0175 2.413 5.96E - 53 13715280 B739_0176 3.0584 1.11E - 20 13715281 B739_0177 1.0467 3.85E - 06 13715373 B739_2137 1.1196 6.02E - 07 13715432 B739_0891 1.0093 1.05E - 06 13715452 B739_0912 1.0968 6.65E - 11 13715453 B739_0913 1.0147 0.0019348 13715513 B739_0973 1.0814 1.74E - 42 13715515 B739_0975 1.0712 4.92E - 15 13715522 B739_0982 1.1625 3.94E - 41 13715525 B739_0985 1.2524 1.07E - 63 13715526 B739_0986 1.0086 2.96E - 104 13715542 -//- 1.4285 1.38E - 29 13715606 B739_1068 3.8593 0 13715627 B739_1089 1.3526 1.76E - 65 13715649 B739_1112 1.0673 5.05E - 41 13715783 B739_1246 1.0718 1.24E - 91 13715836 B739_1299 1.2361 5.75E - 09 13715897 B739_1360 1.3576 0.0002407 13715932 B739_1395 1.4655 1.89E - 17 13715934 B739_1397 1.08 1.36E - 93 13715952 B739_1415 4.7103 0 13715953 B739_1416 3.7691 0 13715954 B739_1417 4.5479 5.15E - 244 13715956 B739_1419 1.2458 2.43E - 15 13716000 B739_1467 1.605 7.16E - 26 13716023 B739_1491 1.2534 2.55E - 67 13716028 B739_1496 1.0255 0.00022217 13716038 B739_1506 1.2051 1.41E - 13 13716056 B739_1525 1.0126 2.76E - 16 13716068 B739_1537 1.1923 2.42E - 35 13716179 B739_1648 1.1687 1.56E - 06 13716365 B739_1842 1.4584 1.63E - 10 13716406 B739_1883 1.1398 2.85E - 14 13716420 B739_1898 1.1221 8.61E - 20 13716438 B739_1916 1.1349 1.80E - 07 13716459 B739_1938 1.0469 7.76E - 115 13716524 B739_2003 1.1565 1.21E - 26 13716533 B739_2012 1.3031 0.0098864 13716610 B739_2089 1.0236 0.00048509 13716613 B739_2092 1.0406 3.79E - 32 13716712 B739_0221 1.0457 3.80E - 21 13716745 B739_0254 1.1712 1.78E - 48 13716748 B739_0257 1.0548 1.69E - 11 13716800 B739_0310 1.1729 4.55E - 21 13716803 B739_0313 1.0601 2.33E - 59 13716804 B739_0314 1.3277 1.60E - 56 13716824 B739_0335 1.2846 9.72E - 16 13716825 B739_0336 1.0435 1.66E - 07 13716826 B739_0337 1.0406 3.10E - 06 13716848 B739_0360 1.2725 1.12E - 137 13716849 B739_0361 1.0413 1.23E - 42 13716885 B739_0397 1.0567 6.51E - 19 13716908 B739_0420 1.0126 2.35E - 05 13716924 B739_0436 1.019 0.00033736 13716964 B739_0476 1.2682 6.15E - 21 13716978 B739_0490 2.3711 4.94E - 95 13717035 B739_0547 1.2256 9.53E - 39 13717082 B739_0594 1.082 1.16E - 21 13717083 B739_0595 2.259 5.94E - 27 13717096 B739_0608 1.6768 3.57E - 11 13717113 B739_0625 1.7097 2.66E - 21 13717239 B739_0753 1.1957 3.41E - 12 13717245 B739_0759 1.1112 2.64E - 14 Gene ID Description 13715178 Hypothetical protein 13715197 Hypothetical protein 13715198 Outer membrane receptor for Fe3+FecA 13715199 Type I deoxyribonuclease HsdR 13715200 Hypothetical protein 13715201 Carbohydrate- binding protein 13715202 Hypothetical protein 13715203 Hypothetical protein 13715204 Hypothetical protein 13715205 Substrate import- associated zinc metallohydrolase 13715206 Glycan metabolism protein RagB 13715207 TonB/linked outer membrane protein, SusC/RagA family 13715231 DNA-binding protein 13715277 TonB-dependent receptor CirA, mostly Fe transport 13715278 Hypothetical protein 13715279 Ankyrin 13715280 Predicted periplasmic protein 13715281 Nitric oxide synthase 13715373 Camphor resistance protein CrcB; integral membrane protein possibly involved in chromosome condensation [cell division and chromosome partitioning] 13715432 Hypothetical protein 13715452 Ribonuclease III 13715453 Hypothetical protein 13715513 50S ribosomal protein L16/L10E 13715515 30S ribosomal protein S17 13715522 50S ribosomal protein L18 13715525 50S ribosomal protein L15 13715526 Preprotein translocase subunit SecY 13715542 tRNA-Glu 13715606 FecA 13715627 Hypothetical protein 13715649 50S ribosomal protein L31 13715783 30S ribosomal protein S16 13715836 Hypothetical protein 13715897 Hypothetical protein 13715932 2-Amino-4-hydroxy- 6- hydroxymethyldihydropteridine pyrophosphokinase 13715934 Outer membrane protein-related peptidoglycan- associated (lipo)protein 13715952 Hypothetical protein 13715953 FepA 13715954 HmuY 13715956 Restriction endonuclease S subunits, Hsds 13716000 Hypothetical protein 13716023 Hypothetical protein 13716028 Hypothetical protein 13716038 Phosphate transport regulator 13716056 OmpA 13716068 Thioredoxin 13716179 Hypothetical protein 13716365 Hypothetical protein 13716406 Preprotein translocase subunit SecG 13716420 3-Oxoacyl-(acyl- carrier-protein) synthase III 13716438 Hypothetical protein 13716459 Hypothetical protein 13716524 Polyisoprenoid- binding protein; YceI-like domain 13716533 Prevent-host-death protein; Antitoxin Phd_YefM, type II toxin-antitoxin system 13716610 Porin 13716613 Starch binding outer membrane protein SusD 13716712 Gliding motility protein GldL 13716745 Hypothetical protein 13716748 Hypothetical protein 13716800 Carbohydrate- binding protein SusD 13716803 Ribonuclease G 13716804 Bacterial nucleoid DNA-binding protein 13716824 Hypothetical protein 13716825 Hypothetical protein 13716826 Ras_like_GTPase 13716848 50S ribosomal protein L11 13716849 Transcription antiterminator 13716885 IMP dehydrogenase/ GMP reductase 13716908 Sec-independent protein secretion pathway component 13716924 Predicted glycosyltransferases 13716964 Hypothetical protein 13716978 Ferritin-like domain 13717035 RNA polymerase Rpb6 13717082 Iron transporter FeoB 13717083 Iron transporter FeoA 13717096 Oxidoreductase; siderophore- interacting protein [inorganic ion transport and metabolism]ViuB 13717113 RNA polymerase sigma factor 13717239 Transthyretin-like protein 13717245 Iron-sulfur binding protein
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|Title Annotation:||Research Article|
|Author:||Liu, MaFeng; Huang, Mi; Zhu, DeKang; Wang, MingShu; Jia, RenYong; Chen, Shun; Sun, KunFeng; Yang, Qi|
|Publication:||BioMed Research International|
|Date:||Jan 1, 2017|
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